AMARETTO_HTMLreport: AMARETTO_HTMLreport

In broadinstitute/ImagingAMARETTO: ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Description

Retrieve an interactive html report, including gene set enrichment analysis if asked for.

Usage

AMARETTO_HTMLreport(AMARETTOinit, AMARETTOresults, ProcessedData,
  show_row_names = FALSE, SAMPLE_annotation = NULL, ID = NULL,
  hyper_geo_reference = NULL, genetic_pert_hyper_geo_reference = NULL,
  chem_pert_hyper_geo_reference = NULL, output_address = "./",
  driverGSEA = TRUE, phenotype_association_table = NULL,
  imaging_phenotypes_keywords = NULL)

Arguments

AMARETTOinit	AMARETTO initialize output
AMARETTOresults	AMARETTO results output
ProcessedData	List of processed input data
show_row_names	if True, sample names will appear in the heatmap
SAMPLE_annotation	SAMPLE annotation will be added to heatmap
ID	ID column of the SAMPLE annotation data frame
hyper_geo_reference	Either GMT file address for genesets or computed GSEA dataframe using HyperGeoEnrichmentTest()
genetic_pert_hyper_geo_reference
chem_pert_hyper_geo_reference
output_address	Output directory for the html files.
driverGSEA	if TRUE, module drivers will also be included in the hypergeometric test.
phenotype_association_table	Optional, Phenotype Association table.
imaging_phenotypes_keywords	a character vector of keywords distinguishing imaging phenotypes.

Value

result

Examples

## Not run: 
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='./')

## End(Not run)

broadinstitute/ImagingAMARETTO documentation built on Dec. 3, 2019, 6:38 p.m.