normMethods: Perform normalizations on Normalyzer dataset

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

Perform normalizations on Normalyzer dataset

Description

Perform normalizations on Normalyzer dataset

Usage

normMethods(
  nds,
  forceAll = FALSE,
  normalizeRetentionTime = TRUE,
  quiet = FALSE,
  rtStepSizeMinutes = 1,
  rtWindowMinCount = 100,
  rtWindowShifts = 1,
  rtWindowMergeMethod = "mean",
  noLogTransform = FALSE
)

Arguments

nds	Normalyzer dataset object.
forceAll	Force all methods to run despite not qualifying for thresholds.
normalizeRetentionTime	Perform retention time based normalization methods.
quiet	Prevent diagnostic output
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	Per default NormalyzerDE performs a log-transformation on the input data. If not needed, specify this option

Value

Returns Normalyzer results object with performed analyzes assigned as attributes

Examples

data(example_summarized_experiment)
normObj <- getVerifiedNormalyzerObject("job_name", example_summarized_experiment)
normResults <- normMethods(normObj)

ComputationalProteomics/NormalyzerDE documentation built on Oct. 18, 2024, 9:57 p.m.