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Annotate modified sites with associated peptides

Source: R/locatePTM.R
locatePTM.Rd

PTMlocate annotates modified sites with associated peptides.

Usage

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

fasta = tidyFasta(system.file("extdata", "O13297.fasta", package="MSstatsPTM"))
locatePTM("DRVSYIHNDSC*TR", "O13297", fasta, "C", "\\*")
#> Key: <uniprot_iso>
#>    uniprot_iso        peptide   site
#>         <char>         <char> <char>
#> 1:      O13297 DRVSYIHNDSC*TR   C467