getcoverage: Get depth of coverage from whole exome sequencing

In CODEX: A Normalization and Copy Number Variation Detection Method for 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

Author(s)

Yuchao Jiang [e-mail]

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

CODEX documentation built on Nov. 8, 2020, 8:22 p.m.