getAlleleCount: Get alternative allele count for positions of interest

In JEFworks/HoneyBADGER: HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data

Description

Get alternative allele count for positions of interest

Usage

getAlleleCount(gr, bamFile, indexFile, verbose = FALSE)

Arguments

gr	GenomicRanges object for positions of interest
bamFile	bam file
indexFile	bai index file
verbose	Boolean of whether or not to print progress and info

Value

refCount reference allele count information for each position of interest altCount alternative allele count information for each position of interest

Examples

## Not run: 
# Sites of interest (chr1:4600000, chr2:2000)
gr <- GRanges(c('chr1', 'chr2'), IRanges(start=c(4600000, 2000), width=1))
# we can get the coverage at these SNP sites from our bams
path <- '../data-raw/bams/'
files <- list.files(path = path)
files <- files[grepl('.bam$', files)]
alleleCounts <- lapply(files, function(f) {
   bamFile <- paste0(path, f)
   indexFile <- paste0(path, paste0(f, '.bai'))
   getAlleleCount(gr, bamFile, indexFile)
})
altCounts <- do.call(cbind, lapply(1:length(gr), function(i) alleleCounts[[i]][[1]]))
refCounts <- do.call(cbind, lapply(1:length(gr), function(i) alleleCounts[[i]][[2]]))
colnames(altCounts) <- colnames(refCounts) <- files

## End(Not run)

JEFworks/HoneyBADGER documentation built on July 24, 2021, 3:01 p.m.