trypsinCleave {spliceSites} | R Documentation |
trypsinCleaves amino acid sequences and returns the fragment which contains the position described by position entry in data.frame.
trypsinCleave(x, minLen=5, ...)
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 |
... |
Additional arguments which may be passed to the routine (currently unused). |
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.
Same class as given object.
Wolfgang Kaisers
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)