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

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)
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the NormalyzerDE package.
#>   Please report the issue to the authors.
#> agg_record_787139172 
#>                    2