consensusScores {BioNet} | R Documentation |
The function calculates consensus scores for a network, given a list of replicate modules.
consensusScores(modules, network, ro=length(modules)/2)
modules |
Calculated modules from pseudo-replicates of expression values in igraph or graphNEL format. |
network |
Interaction network, which shoupld be scores. In igraph or graphNEL format |
ro |
Threshold which is subtracted from the scores to obtain positive and negative value. The default value is half of the number of replicates. |
A result list is returned, consisting of:
N.scores |
Numerical vector node scores. |
E.scores |
Numerical vector edge scores. |
N.frequencies |
Numerical vector node frequencies from the replicate modules. |
E.frequencies |
Numerical vector edge frequencies from the replicate modules. |
Daniela Beisser
library(DLBCL) data(interactome) network <- interactome # precomputed Heinz modules from pseudo-replicates ## Not run: lib <- file.path(.path.package("BioNet"), "extdata") modules <- readHeinzGraph(node.file=file.path(datadir, "ALL_n_resample.txt.0.hnz"), network=network) cons.scores <- consensusScores(modules, network) ## End(Not run)