readMergedBamGaps: Reads an object of type 'gapSites' using a vector of BAM file...

In wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Description

The function takes a vector of BAM-file names and corresponding BAM-index file names. For each given filename, the BAM-file will be opened. The functions uses the bamGapList function (rbamtools) to obtain a data.frame from an bamReader. Values for 'gptm' and 'rpmg' are added. Both are rounded to the number of given digits. The function tests for open connection to BAM-file and for initialized index.

Usage

readMergedBamGaps(infiles,idxInfiles=paste(infiles,".bai",sep=""),digits=3)

Arguments

infiles	character. Name of BAM-files to be opened.
idxInfiles	character. Name of corresponding BAM-index files. Default: paste(infiles,".bai",sep="")
digits	numeric. gptm and rpmg values will be rounded to the number of decimal places given.

Value

gapSites

Author(s)

Wolfgang Kaisers

Examples

bam<-character(2)
bam[1]<-system.file("extdata","rna_fem.bam",package="spliceSites")
bam[2]<-system.file("extdata","rna_mal.bam",package="spliceSites")
mbg<-readMergedBamGaps(bam)

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.