xCodons: xCodon methods

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

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)

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.