generateStatsReport: Generate full output report plot document. Plots p-value...

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

Generate full output report plot document. Plots p-value histograms for each contrast in the NormalyzerStatistics instance and writes these to a PDF report.

Description

Generate full output report plot document. Plots p-value histograms for each contrast in the NormalyzerStatistics instance and writes these to a PDF report.

Usage

generateStatsReport(
  nst,
  jobName,
  jobDir,
  sigThres = 0.1,
  sigThresType = "fdr",
  log2FoldThres = 0,
  plotRows = 3,
  plotCols = 4,
  writeAsPngs = FALSE
)

Arguments

nst	NormalyzerDE statistics object.
jobName	Name of processing run.
jobDir	Path to output directory.
sigThres	Significance threshold for indicating as significant
sigThresType	Type of significance threshold (FDR or p)
log2FoldThres	log2 fold-change required for being counted as significant
plotRows	Number of plot rows.
plotCols	Number of plot columns.
writeAsPngs	Output the report as separate PNG files instead of a single PDF file

Value

None

Examples

data(example_stat_summarized_experiment)
statObj <- NormalyzerStatistics(example_stat_summarized_experiment)
statObj <- calculateContrasts(statObj, comparisons=c("1-2", "2-3"), 
  condCol="group", type="limma")
outputDir <- tempdir()
generateStatsReport(statObj, "jobName", outputDir)

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