annotatePeptides: Annotate peptides with protein ids

Description Usage Arguments Examples

Description

peptides which do not have protein assignment drop out

Usage

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annotatePeptides(pepinfo, fasta, prefix = "(([RK])|(^)|(^M))", suffix = "")

Arguments

pepinfo

- list of peptides - sequence, optional modified sequence, charge state.

fasta

- object as created by readPeptideFasta

prefix

- default "(([RK])|(^)|(^M))"

suffix

- default ""

Examples

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library(prozor)
data(pepprot)

file = file.path(path.package("prozor"),"extdata/shortfasta.fasta" )

fasta = readPeptideFasta(file = file)
res = annotatePeptides(pepprot[1:20,], fasta)
head(res)
res = annotatePeptides(pepprot[1:20,"peptideSeq"],fasta)
length(res)


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