rangeByGeneName {spliceSites}R Documentation

Reads a bamRange object for a given bamReader, refGenome and gene name.

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)

[Package spliceSites version 1.28.0 Index]