.documentFunction {MSstatsTMT} | R Documentation

## A dummy function to store shared documentation items.

### Description

A dummy function to store shared documentation items.

### Usage

    .documentFunction(
      fewMeasurements,
      useUniquePeptide,
      summaryforMultipleRows,
      removeProtein_with1Feature,
      removeProtein_with1Protein,
      removeOxidationMpeptides,
      removeMpeptides
    )

### Arguments

`fewMeasurements` | 'remove'(default) will remove the features that have 1 or 2 measurements across 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.
`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.
`removeOxidationMpeptides` | TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
`removeMpeptides` | TRUE will remove the peptides including 'M' sequence. 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.

### Value

NULL.

[Package MSstatsTMT version 2.0.1 Index]