dnaRanges {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

dnaRanges(x,dnaset,useStrand=TRUE,removeUnknownStrand=TRUE,verbose=TRUE,...)

Arguments

x

cRanges. Range-data will be copied from this object.

dnaset

DNAStringSet. Contains the reference sequence from which the DNA-sequence is extracted.

useStrand

logical. When TRUE, sequences for which strand='-' are reverse-complemented.

removeUnknownStrand

logical. When TRUE, sequences for which strand='-' are removed.

verbose

logical. Determines amount of console output during routine runtime.

...

Optional additional arguments (currently unused).

Value

cdRanges

Author(s)

Wolfgang Kaisers

Examples

bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ga<-alignGapList(reader)
bamClose(reader)
lj<-lJunc(ga,featlen=6,gaplen=6,strand='+')
dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
load(dnafile)
ljd<-dnaRanges(lj,dna_small)
seqlogo(ljd)
[Package spliceSites version 1.31.0 Index]