extractMaxQuant: extractMaxQuant()

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

extractMaxQuant()

Description

Extracts the quantification information from a MaxQuant ProteinGroup.txt file

Usage

extractMaxQuant(
  file = "/filepath/proteinGroups.txt",
  quantification_type = "LFQ",
  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
quantification_type	has to be one of the following options : 'LFQ','Intensity','iBAQ','MS.MS', "TMT","TMT.corrected" Indicate what type of quantification needs to be extracted from the ProteinGroup table, can be either
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
min_peptides	has to be numerical, indicates the minimum number of peptides for protein imporation

Details

This function will extracts the quantification 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 as first column, the other columns will be the Quantitative columns corresponding to the quantitation mode selected.

Author(s)

Geremy Clair

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