% 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]])

)

}