import_dataset_maxquant_evidencetxt: Import a label-free proteomics dataset from MaxQuant

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Import a label-free proteomics dataset from MaxQuant

Description

Import a label-free proteomics dataset from MaxQuant

Usage

import_dataset_maxquant_evidencetxt(
  path,
  collapse_peptide_by = "sequence_modified",
  remove_shared = TRUE
)

Arguments

path	the directory that contains the search results (typically the 'txt' filter that contains files 'proteinGroups.txt' and 'evidence.txt')
collapse_peptide_by	if multiple data points are available for a peptide in a sample, at what level should these be combined? options: "sequence_modified" (recommended default), "sequence_plain", ""
remove_shared	remove all shared peptides that could not be assigned to a single proteingroup as a unique- or razor-peptide ?

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.