annotatePeptides: Annotate peptides with protein ids

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

Annotate peptides with protein ids

Description

peptides which do not have protein assignment drop out

Usage

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

Arguments

pepinfo	- list of peptides - sequence, optional modified sequence, charge state.
fasta	- object as created by readPeptideFasta
peptide	- name of column containing peptide sequences default "peptideSeq"
prefix	- default "(([RK])|(^)|(^M))"
suffix	- default ""

Value

data.frame with columns "peptideSeq", "proteinID","Offset","proteinSequence","matched", "lengthPeptide","proteinlength"

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"))

annotAll = prozor::annotatePeptides(upeptide[seq_len(20)], resCan)
dim(annotAll)

res <-  mutate(annotAll, proteinlength = nchar(proteinSequence))
res <-  select(res, proteinID, peptideSeq, proteinlength, Offset, lengthPeptide)
head(res)

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