trypsinCleave {spliceSites} | R Documentation

## trypsinCleave method

### 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)

[Package spliceSites version 1.28.0 Index]