dot-logSummarizationParams: Log parameters for proteinSummarization function

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

Log parameters for proteinSummarization function

Description

Log parameters for proteinSummarization function

Usage

.logSummarizationParams(
  method,
  global_norm,
  reference_norm,
  remove_norm_channel,
  remove_empty_channel
)

Arguments

method	Four different summarization methods to protein-level can be performed : "msstats"(default), "MedianPolish", "Median", "LogSum".
global_norm	Global median normalization on peptide level data (equalizing the medians across all the channels and MS runs). Default is TRUE. It will be performed before protein-level summarization.
reference_norm	Reference channel based normalization between MS runs on protein level data. TRUE(default) needs at least one reference channel in each MS run, annotated by 'Norm' in Condtion column. It will be performed after protein-level summarization. FALSE will not perform this normalization step. If data only has one run, then reference_norm=FALSE.
remove_norm_channel	TRUE(default) removes 'Norm' channels from protein level data.
remove_empty_channel	TRUE(default) removes 'Empty' channels from protein level data.

Value

TRUE invisibly after logging successfully

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