trypsinCleave: trypsinCleave method

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

Description

trypsinCleaves amino acid sequences and returns the fragment which contains the position described by position entry in data.frame.

Usage

trypsinCleave(x, minLen=5, ...)

Arguments

x	caRanges (aaGapSites). Object in which amino-acid sequences are to be truncated.
minLen	Numeric. Default is 5. Data sets where the remaining sequence fragment is shorter than minLen are excluded.
...	Additional arguments which may be passed to the routine (currently unused).

Details

The routine implements the "Keil"-rule, where sites are described by the regex "[RK](?!P)". The cut position is between [RK] and the following character. The sequence fragment which contains the exon-intron boundary (depicted by position) is returned. Dependent numeric values are recalculated. The returned sequence ends on "[RK]" unless the returned fragment is a sequence suffix.

Value

Same class as given object.

Author(s)

Wolfgang Kaisers

Examples

bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
reader<-bamReader(bam,idx=TRUE)
ga<-alignGapList(reader)
bamClose(reader)
ga
lj<-lJunc(ga,featlen=21,gaplen=21,strand='+')
ljc<-lCodons(lj,frame=1,keepStrand=TRUE)
dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
load(dnafile)
cdr<-dnaRanges(ljc,dna_small)
ar<-translate(cdr)
tra<-truncateSeq(ar)
tyc<-trypsinCleave(tra)

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