ndexr-package: NDEx R client library

In frankkramer-lab/ndexr: NDEx R client library

NDEx R client library

Description

The ndexr package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX objects.

Details

Package:	ndexr
Type:	Package
Version:	1.19.2
Date:	2016-12-02
License:	BSD_3_clause

Author(s)

Florian Auer [e-mail]

Zaynab Hammoud [e-mail]

Frank Kramer [e-mail]

Examples

## Not run: 
require(ndexr)
## login to the NDEx server
ndexcon <- ndex_connect("username", "password")

## search the networks for "EGFR"
networks <- ndex_find_networks(ndexcon, "EGFR")
head(networks, 3)

## UUID of the first search result
networkId <- networks[1,'externalId']
networkId

## get summary of the network
ndex_network_get_summary(ndexcon, networkId)

## get the entire network as RCX object
rcx <- ndex_get_network(ndexcon, networkId)

## show the content (aspects) of the network
rcx$metaData

## visualize the network with RCX
RCX::visualize(rcx)

## upload network as a new network to the NDEx server
networkId <- ndex_create_network(ndexcon, rcx)

## do some other fancy stuff with the network, then
## update the network on the server
networkId <- ndex_update_network(ndexcon, rcx)

## realize, you did bad things to the poor network, so better 
## delete it on the server
ndex_delete_network(ndexcon, networkId)

## End(Not run)

frankkramer-lab/ndexr documentation built on April 4, 2023, 7:19 p.m.