--- a
+++ b/man/AMARETTO_HTMLreport.Rd
@@ -0,0 +1,57 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/amaretto_htmlreport.R
+\name{AMARETTO_HTMLreport}
+\alias{AMARETTO_HTMLreport}
+\title{AMARETTO_HTMLreport}
+\usage{
+AMARETTO_HTMLreport(AMARETTOinit, AMARETTOresults, ProcessedData,
+  show_row_names = FALSE, SAMPLE_annotation = NULL, ID = NULL,
+  hyper_geo_test_bool = FALSE, hyper_geo_reference = NULL,
+  output_address = "./", MSIGDB = TRUE, driverGSEA = TRUE,
+  phenotype_association_table = NULL)
+}
+\arguments{
+\item{AMARETTOinit}{AMARETTO initialize output}
+
+\item{AMARETTOresults}{AMARETTO results output}
+
+\item{ProcessedData}{List of processed input data}
+
+\item{show_row_names}{if True, sample names will appear in the heatmap}
+
+\item{SAMPLE_annotation}{SAMPLE annotation will be added to heatmap}
+
+\item{ID}{ID column of the SAMPLE annotation data frame}
+
+\item{hyper_geo_test_bool}{Boolean if a hyper geometric test needs to be performed. If TRUE provide a GMT file in the hyper_geo_reference parameter.}
+
+\item{hyper_geo_reference}{GMT file with gene sets to compare with.}
+
+\item{output_address}{Output directory for the html files.}
+
+\item{MSIGDB}{TRUE if gene sets were retrieved from MSIGDB. Links will be created in the report.}
+
+\item{driverGSEA}{if TRUE, module drivers will also be included in the hypergeometric test.}
+
+\item{phenotype_association_table}{a Data Frame, containing all modules phenotype association data. Optional.}
+}
+\value{
+result
+}
+\description{
+Retrieve an interactive html report, including gene set enrichment analysis if asked for.
+}
+\examples{
+\dontrun{
+data('ProcessedDataLIHC')
+AMARETTOinit <- AMARETTO_Initialize(ProcessedData = ProcessedDataLIHC,
+                                    NrModules = 2, VarPercentage = 50)
+
+AMARETTOresults <- AMARETTO_Run(AMARETTOinit)
+
+AMARETTO_HTMLreport(AMARETTOinit= AMARETTOinit,AMARETTOresults= AMARETTOresults,
+                    ProcessedData = ProcessedDataLIHC,
+                    hyper_geo_test_bool=FALSE,
+                    output_address='./')
+}
+}