annotateAHO: annotate peptides using AhoCorasickTrie

In prozor: Minimal Protein Set Explaining Peptide Spectrum Matches

Description

peptides which do not have protein assignment drop out

Usage

annotateAHO(pepseq, fasta)

Arguments

pepseq	- list of peptides - sequence, optional modified sequence, charge state.
fasta	- object as created by readPeptideFasta

Value

A data.frame with proteinID, peptideSeq, Offset and proteinSequence

Examples

library(dplyr)

file = system.file("extdata/IDResults.txt.gz" , package = "prozor")
specMeta <- readr::read_tsv(file)
upeptide <- unique(specMeta$peptideSeq)
resCan <-
   prozor::readPeptideFasta(
       system.file("p1000_db1_example/Annotation_canSeq.fasta.gz" , package = "prozor"))
resCanU <- resCan[!duplicated(unlist(resCan))]
annotAll = annotateAHO(upeptide[seq_len(20)], resCanU)
dim(annotAll)

prozor documentation built on Dec. 11, 2021, 9:51 a.m.