import_dataset_metamorpheus: Import a label-free proteomics dataset from MetaMorpheus

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Import a label-free proteomics dataset from MetaMorpheus

Description

Import a label-free proteomics dataset from MetaMorpheus

Usage

import_dataset_metamorpheus(
  path,
  protein_qval_threshold = 0.05,
  collapse_peptide_by = "sequence_modified",
  only_unique_peptides = FALSE
)

Arguments

path	the directory that contains the search results (eg; present files are AllProteinGroups.tsv, AllQuantifiedPeaks.tsv, etc.)
protein_qval_threshold	qvalue threshold for accepting target proteins
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", ""
only_unique_peptides	remove all shared peptides? recommended to leave at FALSE

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