PDtoMSstatsTMTFormat {MSstatsTMT} | R Documentation

## Convert Proteome Discoverer output to MSstatsTMT format.

### Description

Convert Proteome Discoverer output to MSstatsTMT format.

### Usage

    PDtoMSstatsTMTFormat(
      input,
      annotation,
      which.proteinid = "Protein.Accessions",
      useNumProteinsColumn = TRUE,
      useUniquePeptide = TRUE,
      rmPSM_withfewMea_withinRun = TRUE,
      rmProtein_with1Feature = FALSE,
      summaryforMultipleRows = sum,
      use_log_file = TRUE,
      append = FALSE,
      verbose = TRUE,
      log_file_path = NULL,
      ...
    )

### Arguments

`input` | PD report or a path to it.
`annotation` | annotation with Run, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition columns or a path to file. Refer to the example 'annotation' for the meaning of each column.
`which.proteinid` | Use 'Protein.Accessions'(default) column for protein name. 'Master.Protein.Accessions' can be used instead to get the protein name with single protein.
`useNumProteinsColumn` | logical, TURE(default) remove shared peptides by information of # Proteins column in PSM sheet.
`useUniquePeptide` | logical, if TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
`rmPSM_withfewMea_withinRun` | TRUE (default) will remove the features that have 1 or 2 measurements within each Run.
`rmProtein_with1Feature` | TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.
`summaryforMultipleRows` | sum (default) or max - when there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.
`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' of class 'MSstatsTMT'

### Examples

    head(raw.pd)
    head(annotation.pd)
    input.pd <- PDtoMSstatsTMTFormat(raw.pd, annotation.pd)
    head(input.pd)

[Package MSstatsTMT version 2.0.1 Index]