artmsLeaveOnlyUniprotEntryID: Leave only the Entry ID from a typical full Uniprot IDs in a...

In artMS: Analytical R tools for Mass Spectrometry

Description

Downloading a Reference Uniprot fasta database includes several Uniprot IDs for every protein. If the regular expression available in Maxquant is not activated, the full id will be used in the Proteins, Lead Protein, and Leading Razor Protein columns. This script leaves only the Entry ID.

For example, values in a Protein column like this:

sp|P12345|Entry_name;sp|P54321|Entry_name2

will be replace by

'P12345;P54321“

Usage

artmsLeaveOnlyUniprotEntryID(x, columnid)

Arguments

x	(data.frame) that contains the columnid
columnid	(char) Column name with the full uniprot ids

Value

(data.frame) with only Entry IDs.

Examples

# Example of data frame with full uniprot ids and sequences
p <- c("sp|A6NIE6|RN3P2_HUMAN;sp|Q9NYV6|RRN3_HUMAN", 
       "sp|A7E2V4|ZSWM8_HUMAN", 
       "sp|A5A6H4|ROA1_PANTR;sp|P09651|ROA1_HUMAN;sp|Q32P51|RA1L2_HUMAN", 
       "sp|A0FGR8|ESYT2_HUMAN")
s <- c("ALENDFFNSPPRK", "GWGSPGRPK", "SSGPYGGGGQYFAK", "VLVALASEELAK")
evidence <- data.frame(Proteins = p, Sequences = s, stringsAsFactors = FALSE)

# Replace the Proteins column with only Entry ids
evidence <- artmsLeaveOnlyUniprotEntryID(x = evidence, columnid = "Proteins")

artMS documentation built on April 14, 2021, 6 p.m.