MEGENA.ModuleSummary {MEGENA} | R Documentation |
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)