getbambed: Get bam file directories, sample names, and exonic positions

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

Description

Gets bam file directories, sample names from .txt file, and exonic positions from .bed file.

Usage

getbambed(bamdir,bedFile,sampname,projectname,chr)

Arguments

bamdir	Column vector. Each line specifies directory of a bam file. Should be in same order as sample names in sampname.
bedFile	Path to bed file specifying exonic targets. Is of type character.
sampname	Column vector. Each line specifies name of a sample corresponding to the bam file. Should be in same order as bam directories in bamdir.
projectname	String specifying the name of the project. Data will be saved using this as prefix.
chr	Chromosome.

Value

bamdir	Bam directories
sampname	Sample names
ref	IRanges object specifying exonic positions
projectname	String specifying the name of the project.
chr	Chromosome

Author(s)

Yuchao Jiang [e-mail]

References

Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, Morgan M and Carey V (2013). "Software for Computing and Annotating Genomic Ranges." PLoS Computational Biology, 9.

See Also

getcoverage

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

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