writeHeinzNodes: Write node input file for HEINZ

Description Usage Arguments Details Author(s) See Also Examples

View source: R/HeinzUtils.R

Description

Function to write an input file with the node scores for HEINZ. This file is used together with the edge input file to calculate the maximum scoring subnetwork of the graph. The scores are matched by their names to the nodes of the network, therefore if nodes.scores are provided as a vector or matrix, the vector has to be named, respectively the matrix has to be provided with rownames. If the network contains more nodes than the score vector, the nodes without a score are scored with the average over all nodes. If the nodes should not be scored and used for the calculation of the maximum scoring subnetwork, draw a subnetwork subNetwork first and use this for the argument network.

Usage

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writeHeinzNodes(network, file, node.scores=0, use.score=FALSE)

Arguments

network

Network from which to calculate the maximum scoring subnetwork.

file

File to write to.

node.scores

Numeric vector or matrix of scores for the nodes of the network. Names of the vector or rownames of the matrix have to correspond to the PPI identifiers of the network. The scores can also be used from the node attribute "score", given one score for each node.

use.score

Boolean value, whether to use the node attribute "score" in the network as node scores.

Details

Use scoreNodes or scoreFunctionto derive scores from a vector of p-values.

Author(s)

Daniela Beisser

See Also

writeHeinzEdges and writeHeinz

Examples

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#create small network
library(DLBCL)
data(interactome)
small.net <- subNetwork(nodes(interactome)[0:15], interactome)
scores <- c(1:length(nodes(small.net)))
names(scores) <- nodes(small.net)
## Not run: writeHeinzNodes(network=small.net, file="test_nodes", node.scores=scores)

# use Lymphoma data and graph to find module
library(DLBCL)
data(interactome)
data(dataLym)
# get induced subnetwork for all genes contained on the chip
chipGraph <- subNetwork(dataLym$label, interactome)
## Not run: writeHeinzEdges(network=chipGraph, file="lymphoma_edges_001", use.score=FALSE)
score <- dataLym$score001
names(score) <- dataLym$label
## Not run: writeHeinzNodes(network=chipGraph, file="lymphoma_nodes_001", node.scores=score)

BioNet documentation built on Nov. 17, 2017, 9:15 a.m.