keep_longest_isoform_per_gene: Resolving ambiguity in PTM mapping.

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

Description

Typically the downstream use of data is based on gene symbols. One gene symbol may map to multiple UniProt or RefSeq IDs corresponding to different isoforms. This utility simply retains only the longest isoform per gene.

Usage

keep_longest_isoform_per_gene(
  ids,
  gene_id_col,
  isoform_id_col,
  isoform_len_col
)

Arguments

ids	data.frame object. Must contain 3 columns described below.
gene_id_col	character. Name of the column with gene IDs in the 'ids' object.
isoform_id_col	character. Name of the column with protein isoform IDs in the 'ids' object.
isoform_len_col	character. Name of the column with protein isoform lengths.

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", "*")

# Adding gene annotation. Note, this is rat data searched against UniProt.
library(dplyr)
# 10116 is rat taxonomy ID
URL <- "http://www.uniprot.org/uniprot/?query=organism:10116&columns=id,genes(PREFERRED)&format=tab"
ids_with_sites <- read.delim(URL, check.names = F, stringsAsFactors = FALSE) %>%
   rename(GeneMain = "Gene names  (primary )",
          UniProtAcc = "Entry") %>%
   inner_join(ids_with_sites, ., by="UniProtAcc")
nrow(ids_with_sites)
ids_with_sites <- keep_longest_isoform_per_gene(ids_with_sites, 
     "GeneMain", "UniProtAccFull", "ProtLength")
nrow(ids_with_sites)

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