xJunc: xJunc methods: lJunc, rJunc, lrJunc

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

Description

The term 'xJunc' envelopes three functions: lJunc, rJunc and lrJunc. All three functions take a gapSites object and return ranges which are restricted around align-gap (exon-intron) boundaries. The functions lJunc and rJunc return cRanges objects, the lrJunc function returns a gapSites object.

Usage

lJunc(x,featlen,gaplen,unique=FALSE,strand,...)

Arguments

x	gapSites. Object from which the lJunc 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.
unique	Logical. Default is 'FALSE'. When 'TRUE', the function removes duplicate entries which can be due to alternative splice events.
strand	Character. Mandatory. All strand entries are set to the given value.
...	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 junction data
lj<-lJunc(ga,featlen=6,gaplen=6,strand='+')
ljm<-lJunc(ga,featlen=6,gaplen=6,strand='-')
rj<-rJunc(ga,featlen=6,gaplen=6,strand='+')
rjm<-rJunc(ga,featlen=6,gaplen=6,strand='-')
lrj<-lrJunc(ga,lfeatlen=6,rfeatlen=6,strand='+')
lrjm<-lrJunc(ga,lfeatlen=6,rfeatlen=6,strand='-')

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