--- a
+++ b/man/extractPvalues.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/enrichment_functions.R
+\name{extractPvalues}
+\alias{extractPvalues}
+\title{Create a reshaped data frame from multiGSEA output.}
+\usage{
+extractPvalues(enrichmentScores, pathwayNames)
+}
+\arguments{
+\item{enrichmentScores}{Nested List of enrichment scores, calculated by
+multiGSEA function.}
+
+\item{pathwayNames}{List containing Pathway names.}
+}
+\value{
+Data frame where rows are pathways and columns are (adjusted)
+  p-values for each omics layer.
+}
+\description{
+This function reshapes the output from multiGSEA to get a single data frame
+with columns for p-values and adjusted p-values for each omics layer. Each
+row of the data frame represents one pathway.
+}
+\examples{
+# Download pathway definition and extract features
+pathways <- getMultiOmicsFeatures(dbs = c("kegg"), layer = c("transcriptome", "proteome"))
+
+# load omics data and calculate ranks
+data(transcriptome)
+data(proteome)
+ranks <- initOmicsDataStructure(c("transcriptome", "proteome"))
+ranks$transcriptome <- rankFeatures(transcriptome$logFC, transcriptome$pValue)
+names(ranks$transcriptome) <- transcriptome$Symbol
+ranks$proteome <- rankFeatures(proteome$logFC, proteome$pValue)
+names(ranks$proteome) <- proteome$Symbol
+
+# run the enrichment
+es <- multiGSEA(pathways, ranks)
+
+extractPvalues(
+  enrichmentScores = es,
+  pathwayNames = names(pathways[[1]])
+)
+}