AMARETTO_HTMLreport {AMARETTO} | R Documentation

## AMARETTO_HTMLreport

### 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` | a Data Frame, containing all modules phenotype association data. Optional.

### 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)

[Package AMARETTO version 1.2.0 Index]