cAMARETTO_HTMLreport: cAMARETTO_HTMLreport Creates a HTMLreport for the community...

In broadinstitute/ImagingAMARETTO: ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Description

cAMARETTO_HTMLreport

Creates a HTMLreport for the community AMARETTO results

Usage

cAMARETTO_HTMLreport(cAMARETTOresults, cAMARETTOnetworkM,
  cAMARETTOnetworkC, PhenotypeTablesList = NULL, output_address = "./",
  HTMLsAMARETTOlist = NULL, CopyAMARETTOReport = TRUE,
  hyper_geo_reference = NULL, hyper_geo_reference_gp = NULL,
  hyper_geo_reference_cp = NULL, imaging_phenotypes_keywords = NULL,
  driverGSEA = TRUE, NrCores = 2)

Arguments

cAMARETTOresults	The output of the Results function.
cAMARETTOnetworkM	The output of the Module Network function.
cAMARETTOnetworkC	The output of the Identify Communities function.
PhenotypeTablesList	List of Phenotype Association Tables for different AMARETTO runs.
output_address	The output repository for the HTML report.
HTMLsAMARETTOlist	A list with AMARETTO reports to link with the Community AMARETTO report. If NULL, no links are added.
CopyAMARETTOReport	Boolean to indicate if the AMARETTO reports needs to be copied in the AMARETTO report directory. In this way links are contained when moving the HTML directory.
hyper_geo_reference	A reference gmt file to perform the Hyper Geometric Test.
driverGSEA	if TRUE, driver genes beside the target genes will also be included for hypergeometric test.
NrCores	Number of Cores to use during generation of the HTML report.

Value

A set of HTMLs, giving caracteristics of the communities

Examples

cAMARETTO_HTMLreport(cAMARETTOresults,cAMARETTOnetworkM, cAMARETTOnetworkC,HTMLsAMARETTOlist = HTMLsAMARETTOlist, hyper_geo_reference = gmtfile, output_address= "./")

broadinstitute/ImagingAMARETTO documentation built on Dec. 3, 2019, 6:38 p.m.