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

In MEGENA: Multiscale Clustering of Geometrical Network

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.

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.

Value

A data.frame with the columns:

id	gene name
module.parent	parent module id
module	module name.

Author(s)

Won-Min Song

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)

## End(Not run)

MEGENA documentation built on May 1, 2019, 8:07 p.m.