countByGeneName: Reads align number for selected gene from multiple BAM-files.

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

Description

Opens multiple BAM-files and reads aligns for selected gene for each file. The function counts the tag-selected value which either is a BAM-cigar operation (like "N" or "M") or the total number of aligns.

Usage

countByGeneName(object,infiles,idxInfiles=paste(infiles,".bai",sep=""),gene,tag="N")

Arguments

object	Object of class "refGenome"
infiles	Vector of BAM-files
idxInfiles	(Optional) Vector of BAM-index files.
gene	Gene name
tag	Character. Passed to (rbamtools) 'bamCountAll' function. Default value is "N". Other accepted values include "nAligns","M","I","D".

Details

countByGeneName first uses the extractByGeneName and getGenePositions from 'refGenome' in order to calculate coordinates from the given gene name. Then for each given BAM-file name, the functions calls the bamCount function and returns a vector with a count value for each given file. Internally countByGeneName also checks for existing BAM-index file and tries to create index files which do not exist.

Value

Numeric vector. Length equals number of BAM-input files.

Author(s)

Wolfgang Kaisers

Examples

# A) Read filenames
ucf<-system.file("extdata","uc_small.RData",package="spliceSites")
uc<-loadGenome(ucf)
bam<-character(2)
bam[1]<-system.file("extdata","rna_fem.bam",package="spliceSites")
bam[2]<-system.file("extdata","rna_mal.bam",package="spliceSites")
# B) count
countByGeneName(uc,bam,gene="WASH7P",tag="N")
countByGeneName(uc,bam,gene="WASH7P",tag="nAligns")

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