map_PTM_sites: PTM Mapping Utilities

In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

Description

Mapping of PTM location from peptide to fasta file.

Usage

map_PTM_sites(ids, fasta, prot_id_col, peptide_col, mod_char)

Arguments

ids	data.frame object. Must have column containing protein IDs that match names in the provided FASTA file. The other column is peptide IDs containing flanking AAs in the form X.X...X.X
fasta	AAStringSet object. Names must match protein IDs in the corresponding column of the 'ids' object
prot_id_col	character. Name of the column with protein IDs in the 'ids' object.
peptide_col	character. Name of the column with peptides in the 'ids' object.
mod_char	character. Character denoting mapped PTM in peptides. Typically "*".

Examples

fasta_file_name <- system.file("extdata/FASTAs", 
                               "rattus_norvegics_uniprot_2018_09.fasta.gz", 
                               package = "vp.misc")
library(Biostrings)
# FASTA
fst <- readAAStringSet(fasta_file_name, format="fasta", 
                       nrec=-1L, skip=0L, use.names=TRUE)
# extracting UniProt Accessions
names(fst) <- sub("^.*\\|(.*)\\|.*$","\\1",names(fst))

data(phospho_identifications_rat)

ids_with_sites <- map_PTM_sites(ids, fst, "UniProtAccFull", "Peptide", "*")

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.