consensusScores: Calculation of a consensus score for a network

In BioNet: Routines for the functional analysis of biological networks

Description

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

Usage

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

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 Nov. 8, 2020, 5:48 p.m.