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bump version to 0.5.0
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@shajoezhu
shajoezhu committed May 18, 2018
1 parent d6c8a99 commit 09d8b40
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2 changes: 1 addition & 1 deletion .DEploid
Submodule .DEploid updated 47 files
+3 −0 .gitmodules
+6 −2 .travis.yml
+0 −1 COPYING
+674 −0 COPYING
+1 −0 DEploid-Lasso-lib
+12 −0 Dockerfile
+0 −674 LICENSE
+2 −2 Makefile.am
+3 −2 README.md
+1 −1 circle.yml
+5 −6 docs/Citing-DEploid.md
+6 −0 docs/FAQ.md
+19 −0 docs/Pf3k-workflow.md
+160 −71 docs/_build/man/dEploid.1
+ − docs/_static/PD0577-CPanel.IBD.ring.png
+ − docs/_static/scheme.png
+1 −0 docs/conf.py
+0 −14 docs/example.rst
+1 −1 docs/index.rst
+23 −6 docs/input.rst
+2 −3 docs/installation.rst
+7 −35 docs/output.rst
+8 −4 src/dEploid.cpp
+133 −31 src/dEploidIO.cpp
+51 −12 src/dEploidIO.hpp
+9 −1 src/exceptions.hpp
+137 −25 src/export/dEploidIOExport.cpp
+1 −1 src/export/dEploidIOExportPosteriorProb.cpp
+9 −2 src/export/writeMcmcRelated.cpp
+2 −2 src/global.h
+425 −2 src/ibd.cpp
+81 −14 src/ibd.hpp
+65 −254 src/mcmc.cpp
+13 −30 src/mcmc.hpp
+24 −0 src/panel.cpp
+23 −0 src/panel.hpp
+1 −1 src/updateHap.cpp
+0 −2 src/updateHap.hpp
+1 −0 src/variantIndex.hpp
+16 −1 tests/test-against-previous-version.sh
+14 −3 tests/unittest/test_dEploidIO.cpp
+213 −0 tests/unittest/test_ibd.cpp
+9 −79 tests/unittest/test_mcmc.cpp
+1 −1 utilities/DEploidR.R
+57 −23 utilities/dEploidTools.r
+1 −1 utilities/dataExplore.r
+4 −2 utilities/interpretDEploid.r
+1 −1 version
9 changes: 5 additions & 4 deletions DESCRIPTION
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: DEploid
Type: Package
Title: Deconvolute Mixed Genomes with Unknown Proportions
Version: 0.4.4
Version: 0.5.0
Authors@R: c(
person("Joe", "Zhu", role=c("aut", "cre", "cph"), email="[email protected]"),
person('Jacob', 'Almagro-Garcia', role=c('aut', 'cph')),
Expand Down Expand Up @@ -31,13 +31,14 @@ Imports:
Rcpp (>= 0.11.2),
scales (>= 0.4.0),
plotly (>= 4.7.1),
magrittr (>= 1.5)
magrittr (>= 1.5),
rmarkdown(>= 1.6),
htmlwidgets (>= 1.0)
Suggests:
knitr,
rmarkdown,
testthat (>= 0.9.0)
SystemRequirements: C++11
VignetteBuilder: knitr
LinkingTo: Rcpp
RoxygenNote: 6.0.1
Date: 2017-08-09
Date: 2018-05-18
2 changes: 2 additions & 0 deletions NAMESPACE
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@ importFrom("utils", "read.table")
importFrom(Rcpp,evalCpp)
importFrom("magrittr", "%>%")
importFrom("plotly", "plot_ly", "layout", "add_trace")
importFrom("rmarkdown", "pandoc_available")
importFrom("htmlwidgets", "saveWidget")
useDynLib(DEploid, .registration = TRUE)
export(dEploid)
export(plotProportions)
Expand Down
12 changes: 8 additions & 4 deletions src/DEploid/dEploid.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,6 @@

#include <iostream> // std::cout
#include "mcmc.hpp"
#include "panel.hpp"
#include "dEploidIO.hpp"

using namespace std;
Expand All @@ -46,10 +45,13 @@ int main( int argc, char *argv[] ){
return EXIT_SUCCESS;
}

if ( dEploidIO.doPainting() ){
if ( dEploidIO.doComputeLLK() ){
dEploidIO.computeLLKfromInitialHap();
} else if ( dEploidIO.doLsPainting() ){
dEploidIO.chromPainting();
} else{

} else if ( dEploidIO.doIbdPainting() ){
dEploidIO.paintIBD();
}else{
if (dEploidIO.useIBD()){ // ibd
McmcSample * ibdMcmcSample = new McmcSample();
MersenneTwister ibdRg(dEploidIO.randomSeed());
Expand All @@ -66,6 +68,8 @@ int main( int argc, char *argv[] ){
false); // use IBD
mcmcMachinery.runMcmcChain(true, // show progress
false); // use IBD

dEploidIO.paintIBD();
delete mcmcSample;
}
// Finishing, write log
Expand Down
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6 comments on commit 09d8b40

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R/dEploidPlotly.R:28:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:29:32: style: Variable or function name should be snake_case.

​                               potentialOutliers = c()){
                               ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:31:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:33:14: style: Variable or function name should be snake_case.

​    refvsalt$ref.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:35:14: style: Variable or function name should be snake_case.

​    refvsalt$alt.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:107:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:107:32: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:109:3: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:111:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:40: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:177:34: style: Variable or function name should be snake_case.

​                                 potentialOutliers = c()){
                                 ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:179:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$plaf.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~

R/dEploidPlotly.R:181:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$obsWSAF.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~~~~

R/dEploidPlotly.R:236:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:34: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:43: 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_tools.R:46:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(5, 12, 25, 30, 35, 50)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:127:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(1, 10, 20, 30, 40)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:133:55: style: Do not place spaces around code in parentheses or square brackets.

​                 potentialOutliers = potentialOutliers )
                                                      ^

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:28:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:29:32: style: Variable or function name should be snake_case.

​                               potentialOutliers = c()){
                               ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:31:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:33:14: style: Variable or function name should be snake_case.

​    refvsalt$ref.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:35:14: style: Variable or function name should be snake_case.

​    refvsalt$alt.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:107:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:107:32: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:109:3: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:111:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:40: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:177:34: style: Variable or function name should be snake_case.

​                                 potentialOutliers = c()){
                                 ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:179:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$plaf.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~

R/dEploidPlotly.R:181:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$obsWSAF.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~~~~

R/dEploidPlotly.R:236:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:34: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:43: 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_tools.R:46:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(5, 12, 25, 30, 35, 50)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:127:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(1, 10, 20, 30, 40)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:133:55: style: Do not place spaces around code in parentheses or square brackets.

​                 potentialOutliers = potentialOutliers )
                                                      ^

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:28:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:29:32: style: Variable or function name should be snake_case.

​                               potentialOutliers = c()){
                               ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:31:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:33:14: style: Variable or function name should be snake_case.

​    refvsalt$ref.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:35:14: style: Variable or function name should be snake_case.

​    refvsalt$alt.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:107:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:107:32: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:109:3: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:111:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:40: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:177:34: style: Variable or function name should be snake_case.

​                                 potentialOutliers = c()){
                                 ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:179:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$plaf.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~

R/dEploidPlotly.R:181:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$obsWSAF.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~~~~

R/dEploidPlotly.R:236:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:34: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:43: 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_tools.R:46:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(5, 12, 25, 30, 35, 50)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:127:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(1, 10, 20, 30, 40)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:133:55: style: Do not place spaces around code in parentheses or square brackets.

​                 potentialOutliers = potentialOutliers )
                                                      ^

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:28:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:29:32: style: Variable or function name should be snake_case.

​                               potentialOutliers = c()){
                               ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:31:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:33:14: style: Variable or function name should be snake_case.

​    refvsalt$ref.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:35:14: style: Variable or function name should be snake_case.

​    refvsalt$alt.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:107:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:107:32: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:109:3: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:111:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:40: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:177:34: style: Variable or function name should be snake_case.

​                                 potentialOutliers = c()){
                                 ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:179:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$plaf.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~

R/dEploidPlotly.R:181:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$obsWSAF.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~~~~

R/dEploidPlotly.R:236:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:34: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:43: 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_tools.R:46:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(5, 12, 25, 30, 35, 50)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:127:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(1, 10, 20, 30, 40)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:133:55: style: Do not place spaces around code in parentheses or square brackets.

​                 potentialOutliers = potentialOutliers )
                                                      ^

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:28:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:29:32: style: Variable or function name should be snake_case.

​                               potentialOutliers = c()){
                               ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:31:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:33:14: style: Variable or function name should be snake_case.

​    refvsalt$ref.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:35:14: style: Variable or function name should be snake_case.

​    refvsalt$alt.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:107:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:107:32: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:109:3: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:111:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:40: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:177:34: style: Variable or function name should be snake_case.

​                                 potentialOutliers = c()){
                                 ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:179:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$plaf.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~

R/dEploidPlotly.R:181:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$obsWSAF.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~~~~

R/dEploidPlotly.R:236:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:34: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:43: 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_tools.R:46:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(5, 12, 25, 30, 35, 50)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:127:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(1, 10, 20, 30, 40)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:133:55: style: Do not place spaces around code in parentheses or square brackets.

​                 potentialOutliers = potentialOutliers )
                                                      ^

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:28:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:29:32: style: Variable or function name should be snake_case.

​                               potentialOutliers = c()){
                               ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:31:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:33:14: style: Variable or function name should be snake_case.

​    refvsalt$ref.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:35:14: style: Variable or function name should be snake_case.

​    refvsalt$alt.out <- ifelse(rownames(refvsalt) %in%
             ^~~~~~~

R/dEploidPlotly.R:107:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:107:32: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:109:3: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:111:5: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:175:40: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:177:34: style: Variable or function name should be snake_case.

​                                 potentialOutliers = c()){
                                 ^~~~~~~~~~~~~~~~~

R/dEploidPlotly.R:179:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$plaf.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~

R/dEploidPlotly.R:181:16: style: Variable or function name should be snake_case.

​    wsafvsplaf$obsWSAF.out <- ifelse(rownames(wsafvsplaf) %in%
               ^~~~~~~~~~~

R/dEploidPlotly.R:236:1: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:34: style: Variable or function name should be snake_case.

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

R/dEploidPlotly.R:236:43: 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_tools.R:46:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(5, 12, 25, 30, 35, 50)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:127:5: style: Variable or function name should be snake_case.

​    potentialOutliers <- c(1, 10, 20, 30, 40)
    ^~~~~~~~~~~~~~~~~

tests/testthat/test-DEploid_tools.R:133:55: style: Do not place spaces around code in parentheses or square brackets.

​                 potentialOutliers = potentialOutliers )
                                                      ^

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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