OpenSWATHtoMSstatsFormat {MSstats} | R Documentation

## Import OpenSWATH files

### Description

Import OpenSWATH files

### Usage

    OpenSWATHtoMSstatsFormat(
      input,
      annotation,
      filter_with_mscore = TRUE,
      mscore_cutoff = 0.01,
      useUniquePeptide = TRUE,
      removeFewMeasurements = TRUE,
      removeProtein_with1Feature = FALSE,
      summaryforMultipleRows = max,
      use_log_file = TRUE,
      append = FALSE,
      verbose = TRUE,
      log_file_path = NULL,
      ...
    )

### Arguments

`input` | name of MSstats input report from OpenSWATH, which includes feature-level data.
`annotation` | name of 'annotation.txt' data which includes Condition, BioReplicate, Run. Run should be the same as filename.
`filter_with_mscore` | TRUE(default) will filter out the features that have greater than mscore_cutoff in m_score column. Those features will be removed.
`mscore_cutoff` | Cutoff for m_score. Default is 0.01.
`useUniquePeptide` | TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
`removeFewMeasurements` | TRUE (default) will remove the features that have 1 or 2 measurements across runs.
`removeProtein_with1Feature` | TRUE will remove the proteins which have only 1 feature, which is the combination of peptide, precursor charge, fragment and charge. FALSE is default.
`summaryforMultipleRows` | max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
`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.

### Author(s)

Meena Choi, Olga Vitek.

### Examples

    os_raw = system.file("tinytest/raw_data/OpenSWATH/openswath_input.csv",
                                 package = "MSstatsConvert")
    annot = system.file("tinytest/annotations/annot_os.csv",
                        package = "MSstats")
    os_raw = data.table::fread(os_raw)
    annot = data.table::fread(annot)

    os_imported = OpenSWATHtoMSstatsFormat(os_raw, annot, use_log_file = FALSE)
    head(os_imported)

[Package MSstats version 4.0.1 Index]