dnaRanges: 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

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)

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