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+++ b/man/multiGSEA.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/enrichment_functions.R
+\name{multiGSEA}
+\alias{multiGSEA}
+\title{Calculate pathway enrichment for multiple omics layer.}
+\usage{
+multiGSEA(pathways, ranks, eps = 0)
+}
+\arguments{
+\item{pathways}{Nested list containing all pathway features for the
+respective omics layer.}
+
+\item{ranks}{Nested list containing the measured and pre-ranked features for
+each omics layer.}
+
+\item{eps}{This parameter sets the boundary for calculating the p value.}
+}
+\value{
+Nested list containing the enrichment scores for each given pathway
+  and omics layer.
+}
+\description{
+This function calculates GSEA-based enrichments scores for multiple omics
+layer at once. Input pathways or gene sets have to be prepared in advance by
+means of the function \code{\link[multiGSEA]{initOmicsDataStructure}}. The function uses pre-
+ranked lists for each omics layer to calculate the enrichment score. The
+ranking can be calculated by means of the function
+\link[multiGSEA]{rankFeatures}.
+}
+\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
+multiGSEA(pathways, ranks)
+}