annotateAHO: annotate peptides using AhoCorasickTrie

In protViz/prozor: Minimal Protein Set Explaining Peptide Spectrum Matches

annotate peptides using AhoCorasickTrie

Description

peptides which do not have protein assignment drop out

Usage

annotateAHO(pepseq, fasta, peptide = "peptideSeq")

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)

protViz/prozor documentation built on Oct. 17, 2023, 6:39 p.m.