Loads networks from Cytoscape and parses them

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Description

Loads networks from Cytoscape and parses them.

Usage

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getNCIPathways(cyList=NULL, parseNetworks=TRUE, entrezOnly=TRUE, verbose=FALSE)

Arguments

cyList

a list providing the networks loaded from Cytoscape. If NULL, the function will try to build the list from Cytoscape.

verbose

If TRUE, extra information is output.

parseNetworks

A logical. If FALSE, the raw NCI networks are returned as graphNEL objects. If TRUE, some additional parsing is performed by the parseNCInetwork function.

entrezOnly

A logical. If TRUE, only keep nodes with an entrezID property.

Value

A list of two elements: pList, a list of graphNEL objects, and failedW a list containing the names of the networks that R failed to read from cytoscape.

Author(s)

Laurent Jacob

See Also

parseNCInetwork()

Examples

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##------------------------------
## Load NCIgraph
##------------------------------

library(NCIgraph)

##------------------------------
## Example 1: with Cytoscape
##------------------------------

## Must have Cytoscape running with some networks open and Cytoscape RPC plugin started.

## In this case, getNCIPathways will both read the raw networks from Cytoscape and parse them.

## Not run: 
grList <- getNCIPathways(cyList=NULL, parseNetworks=TRUE, entrezOnly=TRUE, verbose=TRUE)$pList

## End(Not run)

##------------------------------
## Example 2: without Cytoscape
##------------------------------

## Get some raw networks

data("NCIgraphVignette", package="NCIgraph")

## When passed a non null cyList argument (a list of networks),
## getNCIPathways will simply parse the list of networks

grList <- getNCIPathways(cyList=NCI.demo.cyList, parseNetworks=TRUE, entrezOnly=TRUE, verbose=TRUE)$pList