R Graphical Manual

Browse All

Last data update: 2014.03.03

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

getbambed

R Documentation

Get bam file directories, sample names, and exonic positions

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 yuchaoj@wharton.upenn.edu

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.

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(CODEX)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: BSgenome.Hsapiens.UCSC.hg19
Loading required package: BSgenome
Loading required package: rtracklayer

Attaching package: 'CODEX'

The following object is masked from 'package:BiocGenerics':

    normalize

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CODEX/getbambed.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getbambed
> ### Title: Get bam file directories, sample names, and exonic positions
> ### Aliases: getbambed
> ### Keywords: package
> 
> ### ** 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
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>