getNCIPathways: Loads networks from Cytoscape and parses them
In NCIgraph: Pathways from the NCI Pathways Database

Description Usage Arguments Value Author(s) See Also Examples

Loads networks from Cytoscape and parses them.

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

`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.

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.

Laurent Jacob

parseNCInetwork()

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

library(NCIgraph)

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

## Must have Cytoscape running with some networks open and CyREST 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