trypsinCleave: trypsinCleave method

Description Usage Arguments Details Value Author(s) Examples

Description

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

Usage

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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

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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.