AMARETTO_HTMLreport {AMARETTO} | R Documentation |
Retrieve an interactive html report, including gene set enrichment analysis if asked for.
AMARETTO_HTMLreport(AMARETTOinit, AMARETTOresults, ProcessedData, SAMPLE_annotation = NULL, ID = NULL, VarPercentage, hyper_geo_test_bool = FALSE, hyper_geo_reference = NULL, output_address = "./", MSIGDB = FALSE, GMTURL = FALSE)
AMARETTOinit |
AMARETTO initialize output |
AMARETTOresults |
AMARETTO results output |
ProcessedData |
List of processed input data |
SAMPLE_annotation |
SAMPLE annotation will be added to heatmap |
ID |
ID column of the SAMPLE annotation data frame |
VarPercentage |
Original Var Percentage used |
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. |
GMTURL |
TRUE if second column of gmt contains URLs to gene set, FALSE if it contains a description |
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, VarPercentage=10,hyper_geo_test_bool=FALSE, output_address='./') ## End(Not run)