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.
generateStatsReport( nst, jobName, jobDir, sigThres = 0.1, sigThresType = "fdr", log2FoldThres = 0, plotRows = 3, plotCols = 4, writeAsPngs = FALSE )
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 |
None
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)