xJuncStrand: xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand

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

Description

The term 'xJuncStrand' envelopes three functions: lJuncStrand, rJuncStrand and lrJuncStrand. All three functions take a gapSites object and return ranges which are restricted around align-gap (exon-intron) boundaries. The functions lJuncStrand and rJuncStrand return cRanges objects, the lrJuncStrand function returns a gapSites object. The resulting objects contain strand information which is copied from the input objects.

Usage

lJuncStrand(x,featlen,gaplen,...)

Arguments

x	gapSites. Object from which the lJuncStrand values are calculated.
featlen	Numeric. Number of nucleotides on feature (exon) side of boundary.
gaplen	Numeric. Number of nucleotides on gap (intron) side of boundary.
...	Optional arguments passed additionally to the function (currently unused).

Details

The functions are intended to provide position information which crosses exon-intron boundaries. Added DNA sequences can be used to produce seqlogos. The functions are intended to be used in advance of xCodons functions. Later on added AA sequences can be used to search for proteins where intronic sequences are retained.

Value

cRanges

Author(s)

Wolfgang Kaisers

Examples

# A) Create gapSites object
bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
reader<-bamReader(bam[1],idx=TRUE)
ga<-alignGapList(reader)
bamClose(reader)
ga

# B) Extract JuncStrandtion data
lj<-lJuncStrand(ga,featlen=6,gaplen=6)
ljm<-lJuncStrand(ga,featlen=6,gaplen=6)
rj<-rJuncStrand(ga,featlen=6,gaplen=6)
rjm<-rJuncStrand(ga,featlen=6,gaplen=6)
lrj<-lrJuncStrand(ga,lfeatlen=6,rfeatlen=6)
lrjm<-lrJuncStrand(ga,lfeatlen=6,rfeatlen=6)

spliceSites documentation built on May 6, 2019, 3:05 a.m.