R/utils_documentation.R

In MeenaChoi/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

#' A dummy function to store shared documentation items.
#' 
#' @import data.table
#' @importFrom MSstatsConvert MSstatsImport MSstatsClean MSstatsPreprocess 
#' MSstatsBalancedDesign MSstatsMakeAnnotation MSstatsLogsSettings
#' 
#' @param removeFewMeasurements TRUE (default) will remove the features that have 1 or 2 measurements across runs.
#' @param useUniquePeptide TRUE (default) removes peptides that are assigned for more than one proteins. 
#' We assume to use unique peptide for each protein.
#' @param summaryforMultipleRows max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities.
#' @param 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.
#' @param removeProtein_with1Peptide TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
#' @param removeOxidationMpeptides TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
#' @param removeMpeptides TRUE will remove the peptides including 'M' sequence. FALSE is default.
#' @param use_log_file logical. If TRUE, information about data processing
#' will be saved to a file.
#' @param append logical. If TRUE, information about data processing will be added
#' to an existing log file.
#' @param verbose logical. If TRUE, information about data processing wil be printed
#' to the console.
#' @param 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.
#' 
#' @keywords internal
#' 
.documentFunction = function() {
    NULL
}