exportPAN: Export inferred PAN or module graphs to files

In PANR: Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

Description

Powered by function write.graph in package igraph, this function writes the inferred PAN or module graphs to files in a variety of formats that are supported by igraph.

Usage

exportPAN(object, file="pan", what="graph", moduleID=1, format="gml", 
verbose=TRUE, ...)

Arguments

object	an object of S4 class PAN.
file	the name of the file to write the graph or module (no need to put a filename extension).
what	a character value specifying what to write: ‘graph’ or ‘pvclustModule’.
moduleID	a numeric or integer vector of modules to write (see details in sigModules).
format	a character value specifying the format to write (see more details in write.graph).
verbose	a logical value to switch on (if TRUE) or off if FALSE detailed run-time message.
...	not in use, but only for further extension.

Value

a numeric vector of ids for significant gene modules

Author(s)

Xin Wang [e-mail]

Examples

## Not run: 
data(bm, package="PANR")
pan<-new("PAN", bm1=bm1)
pan<-infer(pan, para=list(type="SNR", log=TRUE, sign=TRUE, cutoff=log(5)),
filter=FALSE, verbose=TRUE)
data(Bakal2007Cluster, package="PANR")
pan<-buildPAN(pan, engine="igraph", para=list(nodeColor=nodeColor, 
hideNeg=TRUE), verbose=TRUE)
exportPAN(pan, file="pan", what="graph", format="ncol")

## End(Not run)

PANR documentation built on Nov. 8, 2020, 8:15 p.m.