MaxQtoMSstatsFormat: Import MaxQuant files

In MeenaChoi/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Import MaxQuant files

Description

Import MaxQuant files

Usage

MaxQtoMSstatsFormat(
  evidence,
  annotation,
  proteinGroups,
  proteinID = "Proteins",
  useUniquePeptide = TRUE,
  summaryforMultipleRows = max,
  removeFewMeasurements = TRUE,
  removeMpeptides = FALSE,
  removeOxidationMpeptides = FALSE,
  removeProtein_with1Peptide = FALSE,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

evidence	name of 'evidence.txt' data, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Raw.file, Condition, BioReplicate, Run, IsotopeLabelType information.
proteinGroups	name of 'proteinGroups.txt' data. It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'.
proteinID	'Proteins'(default) or 'Leading.razor.protein' for Protein ID.
useUniquePeptide	TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
summaryforMultipleRows	max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
removeFewMeasurements	TRUE (default) will remove the features that have 1 or 2 measurements across runs.
removeMpeptides	TRUE will remove the peptides including 'M' sequence. FALSE is default.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
use_log_file	logical. If TRUE, information about data processing will be saved to a file.
append	logical. If TRUE, information about data processing will be added to an existing log file.
verbose	logical. If TRUE, information about data processing wil be printed to the console.
log_file_path	character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If 'append = TRUE', has to be a valid path to a file.
...	additional parameters to 'data.table::fread'.

Value

data.frame in the MSstats required format.

Note

Warning: MSstats does not support for metabolic labeling or iTRAQ experiments.

Author(s)

Meena Choi, Olga Vitek.

Examples

mq_ev = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_ev.csv",
                                      package = "MSstatsConvert"))
mq_pg = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_pg.csv",
                                      package = "MSstatsConvert"))
annot = data.table::fread(system.file("tinytest/raw_data/MaxQuant/annotation.csv",
                                      package = "MSstatsConvert"))
maxq_imported = MaxQtoMSstatsFormat(mq_ev, annot, mq_pg, use_log_file = FALSE)
head(maxq_imported)

MeenaChoi/MSstats documentation built on May 2, 2024, 10:35 p.m.