AMARETTO_HTMLreport {AMARETTO} | R Documentation |
Retrieve an interactive html report, including gene set enrichment analysis if asked for.
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)
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. |
result
## 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)