ProgenesistoMSstatsFormat {MSstats} | R Documentation

## Import Progenesis files

### Description

Import Progenesis files

### Usage

    ProgenesistoMSstatsFormat(
      input,
      annotation,
      useUniquePeptide = TRUE,
      summaryforMultipleRows = max,
      removeFewMeasurements = TRUE,
      removeOxidationMpeptides = FALSE,
      removeProtein_with1Peptide = FALSE,
      use_log_file = TRUE,
      append = FALSE,
      verbose = TRUE,
      log_file_path = NULL,
      ...
    )

### Arguments

`input` | name of Progenesis output, which is wide-format. 'Accession', 'Sequence', 'Modification', 'Charge' and one column for each run are required.
`annotation` | name of 'annotation.txt' or 'annotation.csv' data which includes Condition, BioReplicate, Run information. It will be matched with the column name of input for MS runs.
`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.
`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.

### Author(s)

Meena Choi, Olga Vitek, Ulrich Omasits

### Examples

    progenesis_raw = system.file("tinytest/raw_data/Progenesis/progenesis_input.csv",
                                 package = "MSstatsConvert")
    annot = system.file("tinytest/raw_data/Progenesis/progenesis_annot.csv",
                        package = "MSstatsConvert")
    progenesis_raw = data.table::fread(progenesis_raw)
    annot = data.table::fread(annot)

    progenesis_imported = ProgenesistoMSstatsFormat(progenesis_raw, annot,
                                                    use_log_file = FALSE)
    head(progenesis_imported)

[Package MSstats version 4.1.1 Index]