saveNetwork: save the subnetwork with global method

In leiming8886/fRNC: ncRNA module search functions

save the subnetwork with global method

Description

The function plots a RNC subnetwork from graphNEL or igraph format. It is used to visualize the modules. For further plotting options use the plot.igraph function of the igraph package. The shapes of the nodes can be changed according to the scores argument

Usage

saveNetwork(
  network,
  name = "network",
  file,
  type = c("table", "XGMML", "sif", "tab")
)

Arguments

network	A graph in igraph or graphNEL format.
name	Name of the network, only needed for the XGMML format.
file	File name to save.
type	Type in which graph shall be saved.

References

Daniela Beisser, Gunnar W. Klau, Thomas Dandekar et al. (2010) BioNet: an R-Package for the functional analysis of biological networks

Examples

## Not run: 
data("dataN")
gene2weight <- combinp(dataN[,c("type","logFC","PValue")])
interac <- interStringency(type = "transcription", spec ="hg",
							stringency = "strict")
interac <- interac[,c("node_gene_ID","type","target_gene_ID")]
res.list_global <- runmodule(network = interac, gene2weight,
								method = "global",FDR = 1e-14)
saveNetwork(res.list_global$module,file="filenames",type = "XGMML")

## End(Not run)

leiming8886/fRNC documentation built on Feb. 21, 2023, 4:12 p.m.