MEGENA.ModuleSummary: MEGENA module summary

In songw01/MEGENA: Multiscale Clustering of Geometrical Network

MEGENA module summary

Description

Summarizes modules into a table.

Usage

MEGENA.ModuleSummary(MEGENA.output,
mod.pvalue = 0.05,hub.pvalue = 0.05,
min.size = 10,max.size = 2500,
annot.table = NULL,symbol.col = NULL,id.col = NULL, 
output.sig = TRUE)

Arguments

MEGENA.output	A list object. The output from "do.MEGENA()".
mod.pvalue	module compactness significance p-value, to identify modules with significant compactness.
hub.pvalue	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.
annot.table	Default value is NULL, indicating no mapping is provided between node names to gene symbols. If provided, the mapping between node names (id.col) and gene symbol (symbol.col) are used.
id.col	column index of annot.table for node names.
symbol.col	column index of annot.table for gene symbols.
output.sig	Default value is TRUE, indicating significant modules are outputted.

Details

output$module.table contains many important information including module hierarchy, as indicated by

Value

A list object with the components:

modules	Final set of modules obtained upon apply mod.pvalue for significance, min.size and max.size for module size thresholding.
mapped.modules	gene symbol mapped modules when "annot.table" is provided.
module.table	data.frame object for module summary table. Columns include: id, module.size, module.parent, module.hub, module.scale and module.pvalue.

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)

## End(Not run)

songw01/MEGENA documentation built on Jan. 19, 2024, 6:51 p.m.