CODEX (version 1.4.0)

getcoverage: Get depth of coverage from whole exome sequencing

Description

Gets depth of coverage for each exon across all samples from whole exome sequencing files.

Usage

getcoverage(bambedObj, mapqthres)

Arguments

bambedObj

Object returned from getbambed

mapqthres

Mapping quality threshold hold of reads.

Value

Y

Read depth matrix

readlength

Vector of read length for each sample

See Also

getbambed

Examples

library(WES.1KG.WUGSC)
dirPath <- system.file("extdata", package = "WES.1KG.WUGSC")
bamFile <- list.files(dirPath, pattern = '*.bam$')
bamdir <- file.path(dirPath, bamFile)
sampnameFile <- file.path(dirPath, "sampname")
sampname <- as.matrix(read.table(sampnameFile))
chr <- 22
bambedObj <- getbambed(bamdir = bamdir, bedFile = file.path(dirPath, 
    "chr22_400_to_500.bed"), sampname = sampname,
    projectname = "CODEX_demo", chr)
bamdir <- bambedObj$bamdir
sampname <- bambedObj$sampname
ref <- bambedObj$ref
projectname <- bambedObj$projectname
chr <- bambedObj$chr
coverageObj <- getcoverage(bambedObj, mapqthres = 20)
Y <- coverageObj$Y
readlength <- coverageObj$readlength