PDtoMSstatsFormat {MSstats} | R Documentation

## Import Proteome Discoverer files

### Description

Import Proteome Discoverer files

### Usage

    PDtoMSstatsFormat(
      input,
      annotation,
      useNumProteinsColumn = FALSE,
      useUniquePeptide = TRUE,
      summaryforMultipleRows = max,
      removeFewMeasurements = TRUE,
      removeOxidationMpeptides = FALSE,
      removeProtein_with1Peptide = FALSE,
      which.quantification = "Precursor.Area",
      which.proteinid = "Protein.Group.Accessions",
      which.sequence = "Sequence",
      use_log_file = TRUE,
      append = FALSE,
      verbose = TRUE,
      log_file_path = NULL,
      ...
    )

### Arguments

`input` | PD report or a path to it.
`annotation` | name of 'annotation.txt' or 'annotation.csv' data which includes Condition, BioReplicate, Run information. 'Run' will be matched with 'Spectrum.File'.
`useNumProteinsColumn` | TRUE removes peptides which have more than 1 in # Proteins column of PD output.
`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.
`which.quantification` | Use 'Precursor.Area'(default) column for quantified intensities. 'Intensity' or 'Area' can be used instead.
`which.proteinid` | Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead.
`which.sequence` | Use 'Sequence'(default) column for peptide sequence. 'Annotated.Sequence' can be used instead.
`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

    pd_raw = system.file("tinytest/raw_data/PD/pd_input.csv",
                         package = "MSstatsConvert")
    annot = system.file("tinytest/annotations/annot_pd.csv", package = "MSstats")
    pd_raw = data.table::fread(pd_raw)
    annot = data.table::fread(annot)

    pd_imported = PDtoMSstatsFormat(pd_raw, annot, use_log_file = FALSE)
    head(pd_imported)

[Package MSstats version 4.1.1 Index]