MEGENA (version 1.3.7)

MEGENA.ModuleSummary: 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.

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.

Details

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

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)
# }