readTabledBamGaps: readTabledBamGaps function

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

Description

readTabledBamGaps

Usage

readTabledBamGaps(infiles,idxInfiles=paste(infiles,".bai",sep=""),prof,rpmg=TRUE)

Arguments

infiles	character. Names of BAM-files.
idxInfiles	character. Names of BAM-index files. When given index file is not found, the function attempts to create a BAM-index file whith the depicted name.
prof	data.frame. Contains group affiliations for each BAM-file. Each column describes an entity by which values are grouped. The row-number in prof must be equal to the number of given BAM-files. The order of BAM infiles and prof defines the group classification for each BAM file. All prof columns must be factors.
rpmg	logical. When TRUE, there will be group specific rpmg align-rates be added to the result table

Details

The function reads gap-align data from all given BAM-files. For each factor level, the number of probes and aligns are counted. When gptm=TRUE also the gptm values are written for each group. The result table contains for each prof factor level 2 (or 3) extra columns.

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")
prof<-data.frame(gender=c("f","m"))
rtbg<-readTabledBamGaps(bam,prof=prof,rpmg=TRUE)
rtbg
getProfile(rtbg)

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