xCodons {spliceSites} | R Documentation

## xCodon methods

### Description

The xCodon functions work on `cRanges` objects. On the contained ranges the function can have two effects: an upstream frame-shift of 0 to 2 positions and a downstream trim to full codons (i.e. (end-start+1)%%3==0). The `lCodon` function acts in '+' strand mode (left frame-shift, right truncation) and the `rCodon` function acts in '-' strand mode (right frame-shift, left truncation).

### Usage

    lCodons(x,frame=1,keepStrand=TRUE)

### Arguments

`x` | cRanges. Object in which codon positions are calculated
`frame` | Numeric. Default is 1. Accepted values are 1,2 or 3. The value causes a frame-shift of size (frame-1).
`keepStrand` | Logical. Default is TRUE. When FALSE, `lCodons` overwrites strand entries by '+' and `rCodons` overwrites strand entries by '-'.

### Details

The function causes an upstream frameshift and a downstream truncation. `lCodon` works with '+'-strand view (left-to-right) and `rCodon` works with '-'-strand view (right to left). The underlying rationale is: The `cRanges` object contains ranges around exon-intron boundaries. The boundary itself is marked by the position value. The functions calculate genomic ranges which can be supplemented by the reference DNA-sequence which then can readily be translated into amino-acid sequences. The different values for `frame` and `keepStrand` are used to produce all six putative amino-acid sequences for this exon-intron boundary.

### Author(s)

Wolfgang Kaisers

### Examples

    bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
    reader<-bamReader(bam,idx=TRUE)
    ga<-alignGapList(reader)
    bamClose(reader)
    dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
    load(dnafile)
    ucf<-system.file("extdata","uc_small.RData",package="spliceSites")
    uc<-loadGenome(ucf)

    lj<-lJunc(ga,featlen=21,gaplen=21,strand='+')
    ljc<-lCodons(lj,frame=1,keepStrand=TRUE)
    rj<-rJunc(ga,featlen=21,gaplen=21,strand='-')
    rjc<-rCodons(rj,frame=1,keepStrand=TRUE)

[Package spliceSites version 1.28.0 Index]