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adding copy right holders to the DESCRIPTION file
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shajoezhu committed Aug 9, 2017
1 parent a429db8 commit 2bfb9d3
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Showing 3 changed files with 14 additions and 3 deletions.
2 changes: 2 additions & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,8 @@

# testthat
^tests/testthat/Rplots.pdf$
^tests/testthat/.*\.png$
^tests/testthat/.*\.html$

# vignettes/
^vignettes/commbine.sh
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9 changes: 8 additions & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,14 @@ Type: Package
Title: Deconvolute Mixed Genomes with Unknown Proportions
Version: 0.4.2
Authors@R: c(
person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="[email protected]")
person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="[email protected]"),
person('Jacob', 'Almagro-Garcia', role=c('aut', 'cph')),
person('Gil', 'McVean', role=c('aut', 'cph')),
person('University of Oxford', '', role=c('cph')),
person('Yinghan', 'Liu', role=c('ctb')),
person('CodeCogs', 'Zyba Ltd', role=c('com', "cph")),
person('Deepak', 'Bandyopadhyay', role=c('com', "cph")),
person('Lutz', 'Kettner', role=c('com', "cph"))
)
Description: Traditional phasing programs are limited to diploid organisms.
Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo
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6 changes: 4 additions & 2 deletions src/r_random_generator.h
Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,11 @@
* dEploid is used for deconvoluting Plasmodium falciparum genome from
* mix-infected patient sample.
*
* Copyright (C) 2016, Sha (Joe) Zhu, Jacob Almagro and Prof. Gil McVean
* Copyright (C) 2016-2017 University of Oxford
*
* This file is part of dEploid.
* Author: Sha (Joe) Zhu
*
* This file is part of DEploid-r.
*
* dEploid is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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9 comments on commit 2bfb9d3

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R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

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R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

@lintr-bot
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R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

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R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

@lintr-bot
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R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

@lintr-bot
Copy link

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R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

@lintr-bot
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

R/dEploidPlotly.R:26:1: style: Variable or function name should be snake_case.

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref"){
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:28:5: style: Variable or function name should be snake_case.

legendName <- "Ref/(Ref+Alt) Ratio"
    ^~~~~~~~~~

R/dEploidPlotly.R:93:1: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:93:32: style: Variable or function name should be snake_case.

plotHistWSAFPlotly <- function(obsWSAF, exclusive = TRUE,
                               ^~~~~~~

R/dEploidPlotly.R:95:3: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
  ^~~~~~~~~~~~

R/dEploidPlotly.R:97:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
    ^~~~~~~~~~~~

R/dEploidPlotly.R:97:27: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                          ^

R/dEploidPlotly.R:97:29: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                            ^

R/dEploidPlotly.R:159:1: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:159:40: style: Variable or function name should be snake_case.

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                       ^~~~~~~

R/dEploidPlotly.R:208:1: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:208:34: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                 ^~~~~~~

R/dEploidPlotly.R:208:43: style: Variable or function name should be snake_case.

plotObsExpWSAFPlotly <- function(obsWSAF, expWSAF,
                                          ^~~~~~~

R/DEploidR.R:23:1: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:23:36: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                   ^~~~~~~~~~~

R/DEploidR.R:23:49: style: Variable or function name should be snake_case.

extractCoverageFromTxt <- function(refFileName, altFileName){
                                                ^~~~~~~~~~~

R/DEploidR.R:54:1: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:54:36: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                   ^~~~~~~~~~~

R/DEploidR.R:54:49: style: Variable or function name should be snake_case.

extractCoverageFromVcf <- function(vcfFileName, ADFieldIndex = 2){
                                                ^~~~~~~~~~~~

R/DEploidR.R:62:5: style: Variable or function name should be snake_case.

numberOfHeaderLines <- 0
    ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:66:13: style: Variable or function name should be snake_case.

numberOfHeaderLines <- numberOfHeaderLines + 1
            ^~~~~~~~~~~~~~~~~~~

R/DEploidR.R:78:5: style: Variable or function name should be snake_case.

sampleName <- names(vcf)[10]
    ^~~~~~~~~~

R/DEploidR.R:83:5: style: Variable or function name should be snake_case.

tmpCovStr <- unlist(lapply(field, `[[`, ADFieldIndex))
    ^~~~~~~~~

R/DEploidR.R:84:5: style: Variable or function name should be snake_case.

tmpCov <- strsplit(as.character(tmpCovStr), ",")
    ^~~~~~

R/DEploidR.R:86:5: style: Variable or function name should be snake_case.

refCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 1)))
    ^~~~~~~~

R/DEploidR.R:87:5: style: Variable or function name should be snake_case.

altCount <- as.numeric(unlist(lapply(tmpCov, `[[`, 2)))
    ^~~~~~~~

R/DEploidR.R:114:1: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
^~~~~~~~~~~

R/DEploidR.R:114:25: style: Variable or function name should be snake_case.

extractPLAF <- function(plafFileName){
                        ^~~~~~~~~~~~

R/DEploidR.R:151:1: style: Variable or function name should be snake_case.

plotProportions <- function(proportions, title = "Components",
^~~~~~~~~~~~~~~

R/DEploidR.R:152:24: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                       ^~~~~~~

R/DEploidR.R:152:37: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                    ^~~~~~~~

R/DEploidR.R:152:51: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                  ^~~~~~~~

R/DEploidR.R:153:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:200:1: style: Variable or function name should be snake_case.

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
^~~~~~~~~~~~

R/DEploidR.R:201:21: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                    ^~~~~~~~~~~

R/DEploidR.R:201:40: style: Variable or function name should be snake_case.

exclude.ref = c(), exclude.alt = c(),
                                       ^~~~~~~~~~~

R/DEploidR.R:202:21: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    ^~~~~~~~~~~~~~~~~

R/DEploidR.R:202:46: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                             ^~~~~~~

R/DEploidR.R:202:59: style: Variable or function name should be snake_case.

potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                                                          ^~~~~~~~

R/DEploidR.R:203:21: style: Variable or function name should be snake_case.

cex.axis = 1){
                    ^~~~~~~~

R/DEploidR.R:207:5: style: Variable or function name should be snake_case.

tmpRange <- 1.1 * mean(max(alt), max(ref))
    ^~~~~~~~

R/DEploidR.R:266:1: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
^~~~~~~~

R/DEploidR.R:266:22: style: Variable or function name should be snake_case.

histWSAF <- function(obsWSAF, exclusive = TRUE,
                     ^~~~~~~

R/DEploidR.R:268:17: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                ^~~~~~~

R/DEploidR.R:268:30: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                             ^~~~~~~~

R/DEploidR.R:268:44: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                           ^~~~~~~~

R/DEploidR.R:269:5: style: Variable or function name should be snake_case.

tmpWSAFIndex <- 1:length(obsWSAF)
    ^~~~~~~~~~~~

R/DEploidR.R:271:9: style: Variable or function name should be snake_case.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
        ^~~~~~~~~~~~

R/DEploidR.R:271:31: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                              ^

R/DEploidR.R:271:33: style: Do not place spaces around code in parentheses or square brackets.

tmpWSAFIndex <- which( ( (obsWSAF < 1) * (obsWSAF > 0)) == 1)
                                ^

R/DEploidR.R:323:1: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
^~~~~~~~~~~~~~

R/DEploidR.R:323:34: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                 ^~~~~~~

R/DEploidR.R:323:43: style: Variable or function name should be snake_case.

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                                          ^~~~~~~

R/DEploidR.R:324:23: style: Variable or function name should be snake_case.

potentialOutliers = c(), title = "WSAF vs PLAF",
                      ^~~~~~~~~~~~~~~~~

R/DEploidR.R:325:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:325:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:325:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:368:1: style: Lines should not be more than 80 characters.

#' prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv$Proportions)[1],]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:373:1: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
^~~~~~~~~~~~~~

R/DEploidR.R:373:28: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                           ^~~~~~~

R/DEploidR.R:373:37: style: Variable or function name should be snake_case.

plotObsExpWSAF <- function(obsWSAF, expWSAF,
                                    ^~~~~~~

R/DEploidR.R:375:23: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                      ^~~~~~~

R/DEploidR.R:375:36: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                   ^~~~~~~~

R/DEploidR.R:375:50: style: Variable or function name should be snake_case.

cex.lab = 1, cex.main = 1, cex.axis = 1){
                                                 ^~~~~~~~

R/DEploidR.R:411:1: style: Variable or function name should be snake_case.

computeObsWSAF <- function(alt, ref){
^~~~~~~~~~~~~~

R/DEploidR.R:432:1: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
^~~~~~~~~~~~~~~~

R/DEploidR.R:432:30: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                             ^~~~~~~~~~~~~~~~~~~~~~

R/DEploidR.R:432:66: style: Variable or function name should be snake_case.

haplotypePainter <- function(posteriorProbabilities, title = "", labelScaling,
                                                                 ^~~~~~~~~~~~

R/DEploidR.R:433:25: style: Variable or function name should be snake_case.

numberOfInbreeding = 0){
                        ^~~~~~~~~~~~~~~~~~

R/DEploidR.R:434:5: style: Variable or function name should be snake_case.

rainbowColorBin <- 16
    ^~~~~~~~~~~~~~~

R/DEploidR.R:435:5: style: Variable or function name should be snake_case.

rainbowColors <- rainbow(rainbowColorBin)
    ^~~~~~~~~~~~~

R/DEploidR.R:437:9: style: Variable or function name should be snake_case.

panelSize <- dim(posteriorProbabilities)[2] - numberOfInbreeding
        ^~~~~~~~~

R/DEploidR.R:438:9: style: Variable or function name should be snake_case.

rainbowColors <- c(rep("#46a8e1", panelSize),
        ^~~~~~~~~~~~~

R/DEploidR.R:446:5: style: Variable or function name should be snake_case.

newXaxt <- round(seq(1, dim(posteriorProbabilities)[1], length.out = 6))
    ^~~~~~~

R/DEploidR.R:449:5: style: Variable or function name should be snake_case.

newYaxt <- seq(0, 1, length.out = 3)
    ^~~~~~~

tests/testthat/test-DEploid_tools.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:7:1: style: Variable or function name should be snake_case.

panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
^~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:9:1: style: Variable or function name should be snake_case.

refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:10:1: style: Variable or function name should be snake_case.

altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
^~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:12:1: style: Variable or function name should be snake_case.

PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:15:1: style: Variable or function name should be snake_case.

PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
^~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:18:1: style: Variable or function name should be snake_case.

expWSAF <- t(PG0390Deconv$Haps) %*% prop
^~~~~~~

tests/testthat/test-DEploid_tools.R:21:5: style: Variable or function name should be snake_case.

PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:44:5: style: Variable or function name should be snake_case.

obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
    ^~~~~~~

tests/testthat/test-dEploid.R:3:1: style: Variable or function name should be snake_case.

vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
^~~~~~~~~~~

tests/testthat/test-dEploid.R:5:1: style: Variable or function name should be snake_case.

plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
^~~~~~~~~~~~

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