annotate peptides with protein ids

Share:

Description

annotate peptides with protein ids

Usage

1
2
annotatePeptides(pepinfo, fasta, digestPattern = "(([RK])|(^)|(^M))",
  mcCores = NULL)

Arguments

pepinfo

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

fasta

- object as created by read.fasta in pacakge seqinr

digestPattern

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

mcCores

number of cores to use

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
library(prozor)
library(doParallel)
library(foreach)
library(seqinr)
data(pepdata)
head(pepdata)

file = file.path(path.package("prozor"),"extdata/shortfasta.fasta" )
fasta = read.fasta(file = file, as.string = TRUE, seqtype="AA")
# we use a subset of the data to speedup the computation
#res = annotatePeptides(pepdata, fasta)
res = annotatePeptides(pepdata[1:20,], fasta,mcCores=1)
head(res)