performNormalizations: Main function for executing normalizations

In ComputationalProteomics/NormalyzerDE: Evaluation of normalization methods and calculation of differential expression analysis statistics

Main function for executing normalizations

Description

Main function for executing normalizations

Usage

performNormalizations(
  nr,
  forceAll = FALSE,
  rtNorm = FALSE,
  rtStepSizeMinutes = 1,
  rtWindowMinCount = 100,
  rtWindowShifts = 1,
  rtWindowMergeMethod = "median",
  noLogTransform = FALSE,
  quiet = FALSE
)

## S4 method for signature 'NormalyzerResults'
performNormalizations(
  nr,
  forceAll = FALSE,
  rtNorm = FALSE,
  rtStepSizeMinutes = 1,
  rtWindowMinCount = 100,
  rtWindowShifts = 1,
  rtWindowMergeMethod = "median",
  noLogTransform = FALSE,
  quiet = FALSE
)

Arguments

nr	Normalyzer results object.
forceAll	Ignore dataset size limits and run all normalizations (only meant for testing purposes)
rtNorm	Perform retention time based normalizations
rtStepSizeMinutes	Retention time normalization window size.
rtWindowMinCount	Minimum number of datapoints in each retention-time segment.
rtWindowShifts	Number of layered retention time normalized windows.
rtWindowMergeMethod	Merge approach for layered retention time windows.
noLogTransform	Prevent log-transforming input
quiet	Don't show regular output messages

Value

nr NormalyzerDE results object

ComputationalProteomics/NormalyzerDE documentation built on Sept. 18, 2023, 9:15 p.m.