xJunc {spliceSites} | R Documentation

## xJunc methods: lJunc, rJunc, lrJunc

### 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='-')

[Package spliceSites version 1.28.0 Index]