locatePTM: Annotate modified sites with associated peptides

Description Usage Arguments Value Examples

View source: R/locatePTM.R

Description

PTMlocate annotates modified sites with associated peptides.

Usage

1
locatePTM(peptide, uniprot, fasta, modResidue, modSymbol, rmConfound = FALSE)

Arguments

peptide

A string vector of peptide sequences. The peptide sequence does not include its preceding and following AAs.

uniprot

A string vector of Uniprot identifiers of the peptides' originating proteins. UniProtKB entry isoform sequence is used.

fasta

A data.table with FASTA information. Output of tidyFasta.

modResidue

A string. Modifiable amino acid residues.

modSymbol

A string. Symbol of a modified site.

rmConfound

A logical. TRUE removes confounded unmodified sites, FALSE otherwise. Default is FALSE.

Value

A data frame with three columns: uniprot_iso, peptide, site.

Examples

1
2
fasta <- tidyFasta(system.file("extdata", "O13297.fasta", package="MSstatsPTM"))
locatePTM("DRVSYIHNDSC*TR", "O13297", fasta, "C", "\\*")

devonjkohler/MSstatsPTM documentation built on Dec. 19, 2021, 11:01 p.m.