generateStatsReport {NormalyzerDE} | R Documentation

## 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)

[Package NormalyzerDE version 1.12.0 Index]