exportPAN: Export inferred PAN or module graphs to files

Description Usage Arguments Value Author(s) Examples

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

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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 [email protected]

Examples

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## 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. 1, 2018, 3:58 a.m.