Description Usage Arguments Value Author(s) Examples
The function calculates consensus scores for a network, given a list of replicate modules.
1 | 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
1 2 3 4 5 6 7 8 9 | 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)
|
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