readTabledBamGaps {spliceSites} | R Documentation

## readTabledBamGaps function

### 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)

[Package spliceSites version 1.28.0 Index]