SPONGE: Sparse Partial Correlations On Gene Expression

View source: R/fn_spongeffects_utility.R

get_central_modules

R Documentation

prepare ceRNA network and network centralities from SPONGE / SPONGEdb

Description

prepare ceRNA network and network centralities from SPONGE / SPONGEdb

Usage

get_central_modules(
  central_nodes,
  node_centrality,
  ceRNA_class = c("lncRNA", "circRNA", "protein_coding"),
  centrality_measure = "Weighted_Degree",
  cutoff = 1000
)

Arguments

`central_nodes`	Vector containing Ensemble IDs of the chosen RNAs to use as central nodes for the modules.
`node_centrality`	output from filter_ceRNA_network() or own measurement, if own measurement taken, please provide node_centrality_column
`ceRNA_class`	default c("lncRNA","circRNA","protein_coding") (see http://www.ensembl.org/info/genome/genebuild/biotypes.html)
`centrality_measure`	Type of centrality measure to use. (Default: "Weighted_Degree", calculated in filter_ceRNA_network())
`cutoff`	the top cutoff modules will be returned (default: 1000)