MaxQtoMSstatsFormat {MSstats} | R Documentation

## 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)

[Package MSstats version 4.1.1 Index]