cAMARETTO_IdentifyCom: cAMARETTO_IdentifyCom

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

Description

cAMARETTO_IdentifyCom

Usage

cAMARETTO_IdentifyCom(
  cAMARETTOnetworkM,
  color_list = NULL,
  filterComm = TRUE,
  ratioCommSize = 0.01,
  MinRuns = 2,
  ratioRunSize = 0.1,
  ratioEdgesInOut = 0.5,
  plot_network = TRUE
)

Arguments

cAMARETTOnetworkM	The output of the Module Network function.
color_list	An optional list with colors.
filterComm	Boolean to indicate if the identified communities needs to be filtered or not.
ratioCommSize	Filter nodes in the community versus nodes out of the community.
MinRuns	Filter on minimum number of runs in the community.
ratioRunSize	Filter on percentage of runs in the community versus total number of runs.
ratioEdgesInOut	Filer on edges in the community versus edges going out.
plot_network	If TRUE, plots the Community Network at the end.

Value

a list with the module network, a community list, community edge information and color list.

Examples

try(
cAMARETTOnetworkC<-cAMARETTO_IdentifyCom(cAMARETTOnetworkM,
filterComm = FALSE)
)

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