exportPAN {PANR}R Documentation

Export inferred PAN or module graphs to files

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 xw264@cam.ac.uk

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)

[Package PANR version 1.30.0 Index]