AMARETTO_HTMLreport: AMARETTO_HTMLreport

In broadinstitute/PerturbationAMARETTO: Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

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_test_bool = FALSE, hyper_geo_reference = NULL,
  output_address = "./", MSIGDB = TRUE, driverGSEA = TRUE,
  phenotype_association_table = 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_test_bool	Boolean if a hyper geometric test needs to be performed. If TRUE provide a GMT file in the hyper_geo_reference parameter.
hyper_geo_reference	GMT file with gene sets to compare with.
output_address	Output directory for the html files.
MSIGDB	TRUE if gene sets were retrieved from MSIGDB. Links will be created in the report.
driverGSEA	if TRUE, module drivers will also be included in the hypergeometric test.
phenotype_association_table

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/PerturbationAMARETTO documentation built on Nov. 4, 2019, 8:14 a.m.