Annotate modified sites with associated peptides

Source: R/locatePTM.R

PTMlocate annotates modified sites with associated peptides.

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("https://www.uniprot.org/uniprot/O13297.fasta")
locatePTM("DRVSYIHNDSC*TR", "O13297", fasta, "C", "\\*")

#>    uniprot_iso        peptide site
#> 1:      O13297 DRVSYIHNDSC*TR C467