R: Generates all possible modification of a given peptide...

genMod {protViz} | R Documentation

## Generates all possible modification of a given peptide seqence and modification pattern

### Description

This function can be used to screen precursor masses for meaningful mass shifts which could correspond to post translational modifications. We suggest to only use a maxiumum of a handful of mass shifts.

### Usage

        genMod(sequences, modificationPattern, nModification=2)

### Arguments

`sequences` | peptide sequences encoded as character sequence using the 20 amino acid letters.
`modificationPattern` | a rbind list structure containing the mono and avg mass as well as the description of a the modifications.
`nModification` | number of maximal modifications.

### Details

t.b.d.

### Author(s)

Hubert Rehrauer and Christian Panse 2012

### Examples

        ptm.0<-cbind(AA="-",
            mono=0.0, avg=0.0, desc="unmodified", unimodAccID=NA)

        ptm.616<-cbind(AA='S',
            mono=-27.010899, avg=NA, desc="Substituition",
                unimodAccID=616)

        ptm.651<-cbind(AA='N',
            mono=27.010899, avg=NA, desc="Substituition",
                unimodAccID=651)

        m<-as.data.frame(rbind(ptm.0, ptm.616, ptm.651))

        genMod(c('TAFDEAIAELDTLNEESYK','TAFDEAIAELDTLSEESYK'), m$AA)

[Package protViz version 0.2.45 Index]