% 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)

}