consensusScores: Calculation of a consensus score for a network

Description Usage Arguments Value Author(s) Examples

View source: R/Resampling.R

Description

The function calculates consensus scores for a network, given a list of replicate modules.

Usage

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consensusScores(modules, network, ro=length(modules)/2)

Arguments

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.

Value

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.

Author(s)

Daniela Beisser

Examples

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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)

BioNet documentation built on May 31, 2017, 3:38 p.m.

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