rangeByGeneName: Reads a bamRange object for a given 'bamReader', 'refGenome'...

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

Description

Locates gene in genome via refGenome and reads a bamRange from the determined region.

Usage

rangeByGeneName(reader,genome,gene,complex=TRUE)

Arguments

reader	Object of class (rbamtools) bamReader. The reader must pass isOpen and index.initialized test.
genome	Object of class (refgenome) refGenome.
gene	Single gene name (character)
complex	Logical. Passed to 'bamRange' function. When TRUE, only aligns with nCigar>1 are counted.

Value

bamRange

Author(s)

Wolfgang Kaisers

Examples

bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ucf<-system.file("extdata","uc_small.RData",package="spliceSites")
uc<-loadGenome(ucf)
range<-rangeByGeneName(reader,uc,"WASH7P")
size(range)

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