DIAUmpiretoMSstatsFormat {MSstats} | R Documentation

## Import DIA-Umpire files

### Description

Import DIA-Umpire files

### Usage

    DIAUmpiretoMSstatsFormat(
      raw.frag,
      raw.pep,
      raw.pro,
      annotation,
      useSelectedFrag = TRUE,
      useSelectedPep = TRUE,
      removeFewMeasurements = TRUE,
      removeProtein_with1Feature = FALSE,
      summaryforMultipleRows = max,
      use_log_file = TRUE,
      append = FALSE,
      verbose = TRUE,
      log_file_path = NULL,
      ...
    )

### Arguments

`raw.frag` | name of FragSummary_date.xls data, which includes feature-level data.
`raw.pep` | name of PeptideSummary_date.xls data, which includes selected fragments information.
`raw.pro` | name of ProteinSummary_date.xls data, which includes selected peptides information.
`annotation` | name of annotation data which includes Condition, BioReplicate, Run information.
`useSelectedFrag` | TRUE will use the selected fragment for each peptide. 'Selected_fragments' column is required.
`useSelectedPep` | TRUE will use the selected peptide for each protein. 'Selected_peptides' column is required.
`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

    diau_frag = system.file("tinytest/raw_data/DIAUmpire/dia_frag.csv",
                                 package = "MSstatsConvert")
    diau_pept = system.file("tinytest/raw_data/DIAUmpire/dia_pept.csv",
                                 package = "MSstatsConvert")
    diau_prot = system.file("tinytest/raw_data/DIAUmpire/dia_prot.csv",
                                 package = "MSstatsConvert")
    annot = system.file("tinytest/annotations/annot_diau.csv",
                        package = "MSstats")
    diau_frag = data.table::fread(diau_frag)
    diau_pept = data.table::fread(diau_pept)
    diau_prot = data.table::fread(diau_prot)
    annot = data.table::fread(annot)
    diau_frag = diau_frag[, lapply(.SD, function(x) if (is.integer(x)) as.numeric(x) else x)]
    # In case numeric columns are not interpreted correctly

    diau_imported = DIAUmpiretoMSstatsFormat(diau_frag, diau_pept, diau_prot,
                                             annot, use_log_file = FALSE)
    head(diau_imported)

[Package MSstats version 4.1.1 Index]