From 2cdc29931dc5d31b654aacdd4bb3ad35367f5527 Mon Sep 17 00:00:00 2001 From: jeffmgranja <106113190+jgranja-cartographybio@users.noreply.github.com> Date: Thu, 21 Jul 2022 18:31:11 -0700 Subject: [PATCH] getGroupFragments --- .DS_Store | Bin 18436 -> 18436 bytes NAMESPACE | 2 +- R/GroupExport.R | 4 ++-- man/addCoAccessibility.Rd | 2 +- man/addGeneScoreMatrix.Rd | 4 ++-- man/addIterativeLSI.Rd | 2 +- man/addMotifAnnotations.Rd | 2 +- man/createArrowFiles.Rd | 2 +- ...GroupFragments.Rd => getGroupFragments.Rd} | 8 ++++---- man/getPeak2GeneLinks.Rd | 2 +- man/plotPeak2GeneHeatmap.Rd | 2 +- 11 files changed, 15 insertions(+), 15 deletions(-) rename man/{exportGroupFragments.Rd => getGroupFragments.Rd} (88%) diff --git a/.DS_Store b/.DS_Store index a41af8c22e2f70c0912d3a93d43797a04ec37501..41725c6111d9c2d2e50fc21cb4b70820fc9e800e 100644 GIT binary patch delta 817 zcma*kOGuPa6bJD0ziNJ8m+aPzIzDO?$;U9(q@m522GTDoajZe;YM8h;n5dThoPG-4Yxw4x2Wup4`E2#3*)BRGyeoW@z4!$n-j2=3uN9$*Yl5XMuy z#(R9gBtGIBQ<%zTG6TzIIV_juu>w}Y+^mXuqR(fT{??}7--}iw^U4O~2?RUa{ed<= z5$m7!GOwztuBk2lhgYJizD$@BG8hw+k~5~*mX?<51Eme%C!P6%n?;-iP{O8^)U@mz zu9rIJhq#E5aB4U$CDp{O=3-S5h%DG0oQqgVs79i*OhyuyWt>_yyUi;U@kkMhlJ&oE ze`5>%aT}w@^nxa6Qo8+=VhWOxA+@Y1f>TOWz>P}jR0j|0;f+xF;Kz0Z&?33oCD#FT zA%uex?I?P13@0Sn8A)~?7jOwzFo3JLh9L~&HtyiAWQ-fdIG*bd3o`Lm?Mh@OJT9*XKAqVE0}J@nLlIrp4UcLgiDmAq6^x@4=%W_P$krB%E_Qd;EpK1Z+D>2ZgO)m&|=9`;fAWE=BBH;dcW z?U1vL#o-5uGN^=_$V?s7OZ#b%Mre#C=q63lBYH|N=?%T7&-8`9(l`2nNJK#c3GqmU z0r@DvGL*rHdNiN~W~@gmEZB}6=ztBro$#Osz3^f$j^HSc;W$p?JVtO4mv9;5xQlzZ zj|Z5BAJ6duZ}9;iF^5n1&SVzNVpt+GusoK}3Ro$tVfCybG&)0gg>B&&4y;97K$~3N zzMdSr%VQ^EXa5bSH?1|T<1K%~>HmhCjSEmEBqnK-7YF>xYwFeLq*h6nlA4yD!S$*w zDOVdvvX*eY5+z(De;~~@aMe_s>ElX-@Ra>&DXBVMsE-LhS5$JYL<(0q*uA<|q@;|B zG|;GT)Hh4Yl%z;f_WWl5#W(Gv8JeYcG$;Ii2{{=$WC^t*l%r0FHK7@6gx5y22{UWZ z%#KcUp&M?&wp*|rz#;VGu)sTsQy9cKL3bgHH;OB`iZM*!1}1R}w{Zs#@dVE>6C6B^ Z{ur6(Hwi_&R!`I&Jkzhet}*`9{09C#wwM3_ diff --git a/NAMESPACE b/NAMESPACE index 3b247ad4..df517f94 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -62,7 +62,6 @@ export(createGenomeAnnotation) export(createLogFile) export(customEnrichment) export(enrichHeatmap) -export(exportGroupFragments) export(exportGroupSE) export(exportPeakMatrixForSTREAM) export(extendGR) @@ -96,6 +95,7 @@ export(getGenes) export(getGenome) export(getGenomeAnnotation) export(getGroupBW) +export(getGroupFragments) export(getGroupSE) export(getGroupSummary) export(getImputeWeights) diff --git a/R/GroupExport.R b/R/GroupExport.R index 4095b38b..a68515b1 100644 --- a/R/GroupExport.R +++ b/R/GroupExport.R @@ -510,11 +510,11 @@ getGroupBW <- function( #' frags <- exportGroupFragments(proj, groupBy = "Clusters") #' #' @export -exportGroupFragments <- function( +getGroupFragments <- function( ArchRProj = NULL, groupBy = "Clusters", threads = getArchRThreads(), - logFile = createLogFile("exportGroupFragments") + logFile = createLogFile("getGroupFragments") ){ #Cell Col Data diff --git a/man/addCoAccessibility.Rd b/man/addCoAccessibility.Rd index c2c601f0..4ff15bc7 100644 --- a/man/addCoAccessibility.Rd +++ b/man/addCoAccessibility.Rd @@ -15,7 +15,7 @@ addCoAccessibility( k = 100, knnIteration = 500, overlapCutoff = 0.8, - maxDist = 1e+05, + maxDist = 100000, scaleTo = 10^4, log2Norm = TRUE, seed = 1, diff --git a/man/addGeneScoreMatrix.Rd b/man/addGeneScoreMatrix.Rd index 76c42d01..cf27e559 100644 --- a/man/addGeneScoreMatrix.Rd +++ b/man/addGeneScoreMatrix.Rd @@ -9,8 +9,8 @@ addGeneScoreMatrix( genes = getGenes(input), geneModel = "exp(-abs(x)/5000) + exp(-1)", matrixName = "GeneScoreMatrix", - extendUpstream = c(1000, 1e+05), - extendDownstream = c(1000, 1e+05), + extendUpstream = c(1000, 100000), + extendDownstream = c(1000, 100000), geneUpstream = 5000, geneDownstream = 0, useGeneBoundaries = TRUE, diff --git a/man/addIterativeLSI.Rd b/man/addIterativeLSI.Rd index 4054082a..2b467c7f 100644 --- a/man/addIterativeLSI.Rd +++ b/man/addIterativeLSI.Rd @@ -26,7 +26,7 @@ addIterativeLSI( sampleCellsFinal = NULL, selectionMethod = "var", scaleTo = 10000, - totalFeatures = 5e+05, + totalFeatures = 500000, filterQuantile = 0.995, excludeChr = c(), keep0lsi = FALSE, diff --git a/man/addMotifAnnotations.Rd b/man/addMotifAnnotations.Rd index b2f97061..2d4fecdd 100644 --- a/man/addMotifAnnotations.Rd +++ b/man/addMotifAnnotations.Rd @@ -11,7 +11,7 @@ addMotifAnnotations( species = NULL, collection = "CORE", motifPWMs = NULL, - cutOff = 5e-05, + cutOff = 0.00005, width = 7, version = 2, force = FALSE, diff --git a/man/createArrowFiles.Rd b/man/createArrowFiles.Rd index ddd9f689..be28b415 100644 --- a/man/createArrowFiles.Rd +++ b/man/createArrowFiles.Rd @@ -13,7 +13,7 @@ createArrowFiles( genomeAnnotation = getGenomeAnnotation(), minTSS = 4, minFrags = 1000, - maxFrags = 1e+05, + maxFrags = 100000, minFragSize = 10, maxFragSize = 2000, QCDir = "QualityControl", diff --git a/man/exportGroupFragments.Rd b/man/getGroupFragments.Rd similarity index 88% rename from man/exportGroupFragments.Rd rename to man/getGroupFragments.Rd index 075f9937..ae11b453 100644 --- a/man/exportGroupFragments.Rd +++ b/man/getGroupFragments.Rd @@ -1,14 +1,14 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/GroupExport.R -\name{exportGroupFragments} -\alias{exportGroupFragments} +\name{getGroupFragments} +\alias{getGroupFragments} \title{Export Group Fragment Files} \usage{ -exportGroupFragments( +getGroupFragments( ArchRProj = NULL, groupBy = "Clusters", threads = getArchRThreads(), - logFile = createLogFile("exportGroupFragments") + logFile = createLogFile("getGroupFragments") ) } \arguments{ diff --git a/man/getPeak2GeneLinks.Rd b/man/getPeak2GeneLinks.Rd index 66c3e3d0..665f9f4c 100644 --- a/man/getPeak2GeneLinks.Rd +++ b/man/getPeak2GeneLinks.Rd @@ -7,7 +7,7 @@ getPeak2GeneLinks( ArchRProj = NULL, corCutOff = 0.45, - FDRCutOff = 1e-04, + FDRCutOff = 0.0001, varCutOffATAC = 0.25, varCutOffRNA = 0.25, resolution = 1, diff --git a/man/plotPeak2GeneHeatmap.Rd b/man/plotPeak2GeneHeatmap.Rd index c6f4d7d8..a3a6b93e 100644 --- a/man/plotPeak2GeneHeatmap.Rd +++ b/man/plotPeak2GeneHeatmap.Rd @@ -7,7 +7,7 @@ plotPeak2GeneHeatmap( ArchRProj = NULL, corCutOff = 0.45, - FDRCutOff = 1e-04, + FDRCutOff = 0.0001, varCutOffATAC = 0.25, varCutOffRNA = 0.25, k = 25,