locatePTM {MSstatsPTM} | R Documentation

## Annotate modified sites with associated peptides

### Description

`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", "\\*")

[Package MSstatsPTM version 1.2.4 Index]