dot-logConverterOptions: Log information about converter options

In Vitek-Lab/MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Log information about converter options

Description

Log information about converter options

Usage

.logConverterOptions(
  feature_columns,
  remove_shared_peptides,
  remove_single_feature_proteins,
  feature_cleaning,
  is_tmt = FALSE
)

Arguments

feature_columns	character vector of names of columns that define spectral features.
remove_shared_peptides	logical, if TRUE shared peptides will be removed.
remove_single_feature_proteins	logical, if TRUE, proteins that only have one feature will be removed.
feature_cleaning	named list with maximum two (for MSstats converters) or three (for MSstatsTMT converter) elements. If handle_few_measurements is set to "remove", feature with less than three measurements will be removed (otherwise it should be equal to "keep"). summarize_multiple_psms is a function that will be used to aggregate multiple feature measurements in a run. It should return a scalar and accept an na.rm parameter. For MSstatsTMT converters, setting remove_psms_with_any_missing will remove features which have missing values in a run from that run.
is_tmt	If TRUE, the dataset comes from a TMT experiment

Value

TRUE invisibly if message was logged

Vitek-Lab/MSstatsConvert documentation built on Nov. 21, 2024, 12:23 p.m.