#' Function for reading in wig file from a pair of samples
#'
#' @export
cnvLogRatio <- function(tumourFile, normalFile, gcFile, mapFile, myChromosome=c(1:22,"X","Y")) {
# Convert reads to IRanges object
tumour_uncorrected_reads <- HMMcopy::wigsToRangedData(tumourFile, gcFile, mapFile)
normal_uncorrected_reads <- HMMcopy::wigsToRangedData(normalFile, gcFile, mapFile)
# Corrected reads by GC-content and mappbility
tumour_corrected_copy <- HMMcopy::correctReadcount(tumour_uncorrected_reads, mappability=0.9,
samplesize=100000)
normal_corrected_copy <- HMMcopy::correctReadcount(normal_uncorrected_reads, mappability=0.9,
samplesize=100000)
# Normalise tumour read counts by normal read counts
res <- tumour_corrected_copy
res$copy <- tumour_corrected_copy$copy - normal_corrected_copy$copy
# Sort by chromosome order
x <- as.data.frame(res)
x$space <- factor(as.character(x$space), levels= myChromosome)
out <- as(x, "RangedData")
return(out)
}
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