writeNormalizedDatasets: Write normalization matrices to file

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

Write normalization matrices to file

Description

Outputs each of the normalized datasets to the specified directory.

Usage

writeNormalizedDatasets(
  nr,
  jobdir,
  includePairwiseComparisons = FALSE,
  includeCvCol = FALSE,
  includeAnovaP = FALSE,
  normSuffix = "-normalized.txt",
  rawdataName = "submitted_rawdata.txt"
)

Arguments

nr	Results object.
jobdir	Path to output directory.
includePairwiseComparisons	Include p-values for pairwise comparisons.
includeCvCol	Include CV column in output.
includeAnovaP	Include ANOVA p-value in output.
normSuffix	String used to name output together with normalization names.
rawdataName	Name of output raw data file.

Value

None

Examples

data(example_summarized_experiment)
normObj <- getVerifiedNormalyzerObject("job_name", example_summarized_experiment)
normResults <- normMethods(normObj)
normResultsWithEval <- analyzeNormalizations(normResults)
outputDir <- tempdir()
writeNormalizedDatasets(normResultsWithEval, outputDir)

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