xJuncStrand {spliceSites} | R Documentation

## xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand

### 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)

[Package spliceSites version 1.28.0 Index]