truncateSeq: truncateSeq method

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

Description

truncateSeqs amino acid sequences at positions depicted by '*' (stop-codon).

Usage

truncateSeq(x,rme=TRUE,trunc=42L)

Arguments

x	caRanges. Object in which amino-acid sequences are to be truncated.
rme	Logical. Default is TRUE. When TRUE, sites with resulting empty sequence (i.e. stop-codon upstream of the splice position) are removed from dataset.
trunc	Integer. ASCII code for character at which truncation should occur. Default value is 42='*' (stop-codon).

Details

The function truncateSeqs the contained amino acid sequences. When the stop-codon is found on the left side of position, the function returns an empty sequence for that site. The position values for these records are also set to 0.

Value

Object of same class as input.

Author(s)

Wolfgang Kaisers

Examples

# A) Read gap-sites from BAM-file
bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ga<-alignGapList(reader)
bamClose(reader)
# B) Load DNA sequence
dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
load(dnafile)
ucf<-system.file("extdata","uc_small.RData",package="spliceSites")
uc<-loadGenome(ucf)
# C) Calculate codon frame data and add DNA
lj<-lJunc(ga,featlen=21,gaplen=21,strand='+')
ljc<-lCodons(lj,frame=1,keepStrand=TRUE)
cdr<-dnaRanges(ljc,dna_small)
# D) Translate DNA to amino acid and truncate
ar<-translate(cdr)
tra<-truncateSeq(ar)

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