lrCodons: lrCodon methods

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

Description

The lrCodon function works on gapSites objects. gapSites manage data on align-gaps which represent data on RNA splice sites. 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 strand argument controls direction of effects: '+' strand mode means left frame-shift and right truncation. '-' strand mode means right frame-shift and left truncation.

Usage

lrCodons(x,frame=1L,strand="+")

Arguments

x	gapSites. 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).
strand	Character or numeric. Default is '+' which is equivalent to 0. Any other value will be interpreted as '-' which is equivalent to 1.

Details

The function causes an upstream frameshift and a downstream truncation. gapSites objects contain data on gap aligns which represent a related pair of exon-intron boundaries. The returned object is of the same class as the input. Supplemented DNA sequence gapSites objects will omit introns and will represent the 'spliced' DNA around the splice site. lrCodon function is intended to shift coordinates, so that the resulting DNA-sequence can readily be translated in a putative amino-acid sequence which contains the splice-site.

Author(s)

Wolfgang Kaisers

Examples

# A) Create gapSites object
bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ga<-alignGapList(reader)
bamClose(reader)

# B) lr-Junctions for '+' -strand
lrj<-lrJunc(ga,lfeatlen=6,rfeatlen=6,strand='+')
lr1<-lrCodons(lrj,frame=1)
lr2<-lrCodons(lrj,frame=2)
lr3<-lrCodons(lrj,frame=3)
lr<-c(lr1,lr2,lr3)

# C) lr-Junctions for '-' -strand
lrj<-lrJunc(ga,lfeatlen=6,rfeatlen=6,strand='-')
lr1<-lrCodons(lrj,frame=1)
lr2<-lrCodons(lrj,frame=2)
lr3<-lrCodons(lrj,frame=3)
lr<-c(lr1,lr2,lr3)

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