AMARETTO_HTMLreport: AMARETTO_HTMLreport

Description Usage Arguments Value Examples

View source: R/amaretto_htmlreport.R

Description

Retrieve an interactive html report, including gene set enrichment analysis if asked for.

Usage

1
2
3
4
5
AMARETTO_HTMLreport(AMARETTOinit, AMARETTOresults, CNV_matrix = NULL,
  MET_matrix = NULL, SAMPLE_annotation = NULL, ID = NULL,
  VarPercentage, hyper_geo_test_bool = FALSE,
  hyper_geo_reference = NULL, output_address = "./", MSIGDB = FALSE,
  GMTURL = FALSE)

Arguments

AMARETTOinit

AMARETTO initialize output

AMARETTOresults

AMARETTO results output

CNV_matrix

Processed CNV matrix ($CNV_matrix element from Preprocess_CancerSite() list output).

MET_matrix

Processed methylation matrix ($MET_matrix element from Preprocess_CancerSite() list output).

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

Value

result

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
## Not run: 
data('ProcessedDataLIHC')
AMARETTOinit <- AMARETTO_Initialize(MA_matrix = ProcessedDataLIHC$MA_matrix,
                                    CNV_matrix = ProcessedDataLIHC$CNV_matrix,
                                    MET_matrix = ProcessedDataLIHC$MET_matrix,
                                    NrModules = 20, VarPercentage = 60)

AMARETTOresults <- AMARETTO_Run(AMARETTOinit)

AMARETTO_HTMLreport(AMARETTOinit= AMARETTOinit,AMARETTOresults= AMARETTOresults,
                    CNV_matrix=ProcessedDataLIHC$CNV_matrix,
                    MET_matrix = ProcessedDataLIHC$MET_matrix,
                    VarPercentage=10,hyper_geo_test_bool=FALSE,
                    output_address='./')

## End(Not run)

gevaertlab/AMARETTO documentation built on Feb. 19, 2019, 4:15 a.m.