dot-documentFunction: A dummy function to store shared documentation items.

In Vitek-Lab/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

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.

Vitek-Lab/MSstatsTMT documentation built on Nov. 18, 2024, 11:30 a.m.