writeHeinzEdges: Write edge input file for HEINZ

Description Usage Arguments Author(s) See Also Examples

View source: R/HeinzUtils.R

Description

Function to write an input file for HEINZ with edge scores. If no edge scores are used, they are set to 0. In order to run HEINZ, a node input and edge input file are needed.

Usage

1
writeHeinzEdges(network, file, edge.scores=0, use.score=FALSE)

Arguments

network

Network from which to calculate the maximum scoring subnetwork.

file

File to write to.

edge.scores

Numeric vector of scores for the edges of the network. Edge scores have to be given in the order of the edges in the network. It is better to append the edge scores as the edge attribute "score" to the network: V(network)\$score and set use.score to TRUE.

use.score

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

Author(s)

Daniela Beisser

See Also

writeHeinzNodes and writeHeinz

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
library(DLBCL)
# use Lymphoma data and graph to find module
data(interactome)
data(dataLym)
# get induced subnetwork for all genes contained on the chip
chipGraph <- subNetwork(dataLym$label, interactome)
# remove self loops
graph <- rmSelfLoops(chipGraph)
## Not run: writeHeinzEdges(network=graph, file="lymphoma_edges_001", use.score=FALSE)
score <- dataLym$score001
names(score) <- dataLym$label
## Not run: writeHeinzNodes(network=graph, file="lymphoma_nodes_001", node.scores=score)


# write another edge file with edge scores 
library(igraph)
data(interactome)
interactome <- igraph.from.graphNEL(interactome)
small.net <- subNetwork(V(interactome)[1:16]$name, interactome)
scores <- c(1:length(E(small.net)))
E(small.net)$score <- scores
## Not run: writeHeinzEdges(network=small.net, file="test_edges", use.score=TRUE)

BioNet documentation built on May 2, 2018, 4:16 a.m.