removeNodes: This function gracefully removes nodes from a regulatory...

In frankkramer-lab/rBiopaxParser: Parses BioPax files and represents them in R

Description

This function gracefully removes nodes from a regulatory graph. If the node to be removed has both parent and child nodes, these are connected directly. The weight of the new direct edge is the product of multiplying the incomming and outgoing edge weights of the original node.

Usage

removeNodes(graph, nodes)

Arguments

graph	graphNEL
nodes	vector of node names specifiying which nodes to remove.

Value

Returns a graph with specified nodes removed.

Author(s)

Frank Kramer

Examples

 # load data and retrieve wnt pathway
 data(biopaxexample)
 pwid1 = "pid_p_100002_wntpathway"
 mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
 mygraph1 = layoutRegulatoryGraph(mygraph1)
 # retrieve all nodes
 nodes = nodes(mygraph1)
 # random expression data for your nodes 
 values = rnorm(length(nodes), mean=6, sd=2)
 # color nodes of the graph
 mygraph1 = colorGraphNodes(mygraph1, nodes, values, colors="greenred") 
 # plot the now colored graph 
 plotRegulatoryGraph(mygraph1, layoutGraph=FALSE)

frankkramer-lab/rBiopaxParser documentation built on July 19, 2020, 9:49 a.m.