extractMaxQuantIDs: extractMaxQuantIDs()

In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines

extractMaxQuantIDs()

Description

Extracts the IDs information from a MaxQuant ProteinGroup.txt file

Usage

extractMaxQuantIDs(
  file = "/filepath/proteinGroups.txt",
  cont.rm = TRUE,
  site.rm = TRUE,
  rev.rm = TRUE,
  min_peptides = 1,
  min_unique_peptides = 1,
  min_razor_peptides = 1
)

Arguments

file	This has to be the file path and file name of the maxQuant proteinGroup.txt file from which the information has to be extracted
cont.rm	has to be TRUE or FALSE, indicates if the contaminant have to be removed
site.rm	has to be TRUE or FALSE, indicates if the identification by site only have to be removed
rev.rm	has to be TRUE or FALSE, indicates if the False Positive entries have to be removed

Details

This function will extracts the IDs information from one quantification time of a MaxQuant ProteinGroup.txt file.

Value

it will return a data.frame with a first column containing the Protein IDs the following columns will be the following : 'majority.protein.ids', 'fasta.headers', 'peptide.counts.all','peptide.counts.razor.unique','peptide.counts..unique.','fasta.headers','number.of.proteins','peptides','razor...unique.peptides', 'unique.peptides'

Author(s)

Geremy Clair

PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.