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Option to turn off the chrX Normalization in createPanelOfNormals.R #91

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Option to turn off the chrX Normalization in createPanelOfNormals.R #91

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f5888c6
Added logical option to createPanelOfNormals.R to turn the Normalize …
Jan 27, 2021
b65ded1
Adding support for selecting species, defaults to human though
bryce-turner Apr 26, 2021
282637f
Merge pull request #1 from bryce-turner/master
Apr 27, 2021
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4 changes: 2 additions & 2 deletions R/utils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@ filterEmptyChr <- function(gr){
####################################
##### FUNCTION GET SEQINFO ######
####################################
getSeqInfo <- function(genomeBuild = "hg19", genomeStyle = "NCBI"){
bsg <- paste0("BSgenome.Hsapiens.UCSC.", genomeBuild)
getSeqInfo <- function(genomeSpecies = "Hsapiens", genomeBuild = "hg19", genomeStyle = "NCBI"){
bsg <- paste0("BSgenome.", genomeSpecies, ".", genomeStyle, ".", genomeBuild)
if (!require(bsg, character.only=TRUE, quietly=TRUE, warn.conflicts=FALSE)) {
seqinfo <- Seqinfo(genome=genomeBuild)
} else {
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9 changes: 6 additions & 3 deletions scripts/createPanelOfNormals.R
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Expand Up @@ -17,7 +17,8 @@ option_list <- list(
make_option(c("--chrNormalize"), type="character", default="c(1:22)", help = "Specify chromosomes to normalize GC/mappability biases"),
make_option(c("--maleChrXLogRThres"), type="numeric", default=-0.80, help = "ChrX Log ratio threshold to confirm as male gender."),
make_option(c("-e", "--exons.bed"), type = "character", default=NULL, help = "Path to bed file containing exon regions."),
make_option(c("--method"), type = "character", default="median", help="Median or Mean.")
make_option(c("--method"), type = "character", default="median", help="Median or Mean."),
make_option(c("--normalizeX"), type="logical", default=TRUE, help = "Normalize chrX by median. Default: [%default]")
#make_option(c("--ylim"), type = "character", default="c(-2,2)", help="Y-limits for plotting of mean/median log ratios")
)
parseobj <- OptionParser(option_list=option_list)
Expand All @@ -35,6 +36,7 @@ outfile <- opt$outfile
genomeStyle <- opt$genomeStyle
#ylim <- eval(parse(text = opt$ylim))
maleChrXLogRThres <- opt$maleChrXLogRThres
normalizeX <- as.logical(opt$normalizeX)
chrs <- as.character(eval(parse(text = opt$chrs)))
chrNormalize <- as.character(eval(parse(text=opt$chrNormalize)));
seqlevelsStyle(chrs) <- genomeStyle
Expand Down Expand Up @@ -94,8 +96,9 @@ for (i in 1:length(files)){
chrXStr <- grep("X", chrs, value = TRUE)
chrXInd <- as.character(seqnames(normalGR)) == chrXStr
## Normalize chrX ##
values(normalGR)[[sid]][chrXInd] <- values(normalGR)[[sid]][chrXInd] - chrXMedian

if (normalizeX){
values(normalGR)[[sid]][chrXInd] <- values(normalGR)[[sid]][chrXInd] - chrXMedian
}
}


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4 changes: 3 additions & 1 deletion scripts/runIchorCNA.R
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Expand Up @@ -45,6 +45,7 @@ option_list <- list(
make_option(c("--chrs"), type="character", default="c(1:22,\"X\")", help = "Specify chromosomes to analyze. Default: [%default]"),
make_option(c("--genomeBuild"), type="character", default="hg19", help="Geome build. Default: [%default]"),
make_option(c("--genomeStyle"), type = "character", default = "NCBI", help = "NCBI or UCSC chromosome naming convention; use UCSC if desired output is to have \"chr\" string. [Default: %default]"),
make_option(c("--genomeSpecies"), type="character", default="Hsapiens", help="Geome species. Default: [%default]"),
make_option(c("--normalizeMaleX"), type="logical", default=TRUE, help = "If male, then normalize chrX by median. Default: [%default]"),
make_option(c("--minTumFracToCorrect"), type="numeric", default=0.1, help = "Tumor-fraction correction of bin and segment-level CNA if sample has minimum estimated tumor fraction. [Default: %default]"),
make_option(c("--fracReadsInChrYForMale"), type="numeric", default=0.001, help = "Threshold for fraction of reads in chrY to assign as male. Default: [%default]"),
Expand Down Expand Up @@ -106,6 +107,7 @@ gender <- NULL
outImage <- paste0(outDir,"/", patientID,".RData")
genomeBuild <- opt$genomeBuild
genomeStyle <- opt$genomeStyle
genomeSpecies <- opt$genomeSpecies
chrs <- as.character(eval(parse(text = opt$chrs)))
chrTrain <- as.character(eval(parse(text=opt$chrTrain)));
chrNormalize <- as.character(eval(parse(text=opt$chrNormalize)));
Expand All @@ -125,7 +127,7 @@ if (!is.null(libdir) && libdir != "None"){
}

## load seqinfo
seqinfo <- getSeqInfo(genomeBuild, genomeStyle)
seqinfo <- getSeqInfo(genomeSpecies, genomeBuild, genomeStyle)

if (substr(tumour_file,nchar(tumour_file)-2,nchar(tumour_file)) == "wig") {
wigFiles <- data.frame(cbind(patientID, tumour_file))
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