PTMlocate: Annotate modified sites with associated peptides

In tsunghengtsai/MSstatsPTM: Statistical Characterization of Post-translational Modifications

Description

PTMlocate annotates modified sites with associated peptides.

Usage

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

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.