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

In broadinstitute/CommunityAMARETTO: CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Description

cAMARETTO_HTMLreport Creates a HTMLreport for the community AMARETTO results

Usage

cAMARETTO_HTMLreport(
  cAMARETTOresults = list(),
  cAMARETTOnetworkM = list(),
  cAMARETTOnetworkC = list(),
  PhenotypeTablesList = NULL,
  output_address = "./",
  HTMLsAMARETTOlist = NULL,
  CopyAMARETTOReport = TRUE,
  hyper_geo_reference = NULL,
  hyper_geo_reference_gp = NULL,
  hyper_geo_reference_cp = 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.
hyper_geo_reference_gp	Hypergeometric test table for genetic perturbation
hyper_geo_reference_cp	Hypergeometric test table for chemical perturbation
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

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

broadinstitute/CommunityAMARETTO documentation built on April 6, 2020, 10:44 p.m.