getcoverage: Get depth of coverage from whole exome sequencing

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

1
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 yuchaoj@wharton.upenn.edu

See Also

getbambed

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
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


Search within the CODEX package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.