gene.table: Gene symbols associated to protein accessions

In msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts

Description

Given a character vector with protein accessions, and a character vector with protein descriptions including gene symbols, returns a character vector with gene symbols whose names are the protein accessions. A character pattern should also be given to match the gene symbols.

Usage

gene.table(Accession, Protein, patt = "GN=[A-Z0-9_]*", off = 3)

Arguments

Accession	A character vector with protein accessions
Protein	A character vector of protein descriptions including gene name symbols.
patt	A character pattern to match the gene symbol within the protein description.
off	Offset from the first character in the pattern corresponding to the gene symbol.

Details

NA is inserted where no match is found

Value

A character vector with gene symbols, whose names are the corresponding protein accessions.

Author(s)

Josep Gregori

Examples

data(pnms)
head(pnms)
gene.smb <- gene.table(pnms$Accession,pnms$Proteins)
head(gene.smb)

msmsEDA documentation built on Nov. 8, 2020, 6:55 p.m.