MEGENA (version 1.3.7)

module_convert_to_table: conversion of module list object to a data.frame table format

Description

Summarizes module hub/hierarchy/membership into a data.frame table format.

Usage

module_convert_to_table(MEGENA.output,mod.pval = 0.05,
hub.pval = 0.05,min.size = 10,max.size)

Arguments

MEGENA.output

A list object. The output from "do.MEGENA()".

mod.pval

module compactness significance p-value, to identify modules with significant compactness.

hub.pval

node degree significance p-value to identify nodes with significantly high degree.

min.size

minimum module size allowed to finalize in the summary output.

max.size

maximum module size allowed to finalize in the summary output.

Value

A data.frame with the columns:

id

gene name

module.parent

parent module id

module

module name.

Details

the resulting data.frame contains the following essential columns: id, module.parent and module. If the co-expression network bears significant hubs, it will additionally have node.degree (connectivity), node.strength (sum of edge weights) and is.hub column to supplement hub information.

Examples

# NOT RUN {
rm(list = ls())
data(Sample_Expression)
ijw <- calculate.correlation(datExpr[1:100,],doPerm = 2)
el <- calculate.PFN(ijw[,1:3])
g <- graph.data.frame(el,directed = FALSE)
MEGENA.output <- do.MEGENA(g = g,remove.unsig = FALSE,doPar = FALSE,n.perm = 10)
output.summary <- MEGENA.ModuleSummary(MEGENA.output,
mod.pvalue = 0.05,hub.pvalue = 0.05,
min.size = 10,max.size = 5000,
annot.table = NULL,id.col = NULL,symbol.col = NULL,
output.sig = TRUE)
module.df = module_convert_to_table(MEGENA.output,mod.pval = 0.05,
hub.pval = 0.05,min.size = 10,max.size)
head(module.df)
# }