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b/man/AMARETTO_HTMLreport.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/amaretto_htmlreport.R |
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\name{AMARETTO_HTMLreport} |
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\alias{AMARETTO_HTMLreport} |
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\title{AMARETTO_HTMLreport} |
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\usage{ |
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AMARETTO_HTMLreport(AMARETTOinit, AMARETTOresults, ProcessedData, |
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show_row_names = FALSE, SAMPLE_annotation = NULL, ID = NULL, |
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hyper_geo_test_bool = FALSE, hyper_geo_reference = NULL, |
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output_address = "./", MSIGDB = TRUE, driverGSEA = TRUE, |
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phenotype_association_table = NULL) |
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} |
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\arguments{ |
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\item{AMARETTOinit}{AMARETTO initialize output} |
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\item{AMARETTOresults}{AMARETTO results output} |
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\item{ProcessedData}{List of processed input data} |
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\item{show_row_names}{if True, sample names will appear in the heatmap} |
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\item{SAMPLE_annotation}{SAMPLE annotation will be added to heatmap} |
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\item{ID}{ID column of the SAMPLE annotation data frame} |
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\item{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.} |
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\item{hyper_geo_reference}{GMT file with gene sets to compare with.} |
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\item{output_address}{Output directory for the html files.} |
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\item{MSIGDB}{TRUE if gene sets were retrieved from MSIGDB. Links will be created in the report.} |
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\item{driverGSEA}{if TRUE, module drivers will also be included in the hypergeometric test.} |
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\item{phenotype_association_table}{a Data Frame, containing all modules phenotype association data. Optional.} |
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} |
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\value{ |
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result |
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} |
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\description{ |
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Retrieve an interactive html report, including gene set enrichment analysis if asked for. |
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} |
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\examples{ |
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\dontrun{ |
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data('ProcessedDataLIHC') |
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AMARETTOinit <- AMARETTO_Initialize(ProcessedData = ProcessedDataLIHC, |
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NrModules = 2, VarPercentage = 50) |
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AMARETTOresults <- AMARETTO_Run(AMARETTOinit) |
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AMARETTO_HTMLreport(AMARETTOinit= AMARETTOinit,AMARETTOresults= AMARETTOresults, |
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ProcessedData = ProcessedDataLIHC, |
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hyper_geo_test_bool=FALSE, |
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output_address='./') |
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} |
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} |