PTMlocate: Annotate modified sites with associated peptides

Description Usage Arguments Value Examples

View source: R/locate.R

Description

PTMlocate annotates modified sites with associated peptides.

Usage

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PTMlocate(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 tibble 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

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fasta <- tidyFasta("https://www.uniprot.org/uniprot/O13297.fasta")
PTMlocate("DRVSYIHNDSC*TR", "O13297", fasta, "C", "\\*")

tsunghengtsai/MSstatsPTM documentation built on Oct. 4, 2020, 5:51 p.m.