comparemodulestwonets {MODA}R Documentation

Illustration of two networks comparison

Description

Compare the background network and a condition-specific network. A Jaccard index is used to measure the similarity of two sets, which represents the similarity of each module pairs from two networks.

Usage

comparemodulestwonets(sourcehead, nm1, nm2, ind1, ind2)

Arguments

sourcehead

prefix of where to store results

nm1

how many modules in the background network

nm2

how many modules in the condition-specific network

ind1

indicator of the background network

ind2

indicator of the condition-specific network

Value

A matrix where each entry is the Jaccard index of corresponding modules from two networks

Author(s)

Dong Li, dxl466@cs.bham.ac.uk

Examples

data(synthetic)
ResultFolder = 'ForSynthetic' # where middle files are stored
CuttingCriterion = 'Density' # could be Density or Modularity
indicator1 = 'X'     # indicator for data profile 1
indicator2 = 'Y'      # indicator for data profile 2
intModules1 <- WeightedModulePartitionHierarchical(datExpr1,ResultFolder,
indicator1,CuttingCriterion) 
intModules2 <- WeightedModulePartitionHierarchical(datExpr2,ResultFolder,
indicator2,CuttingCriterion) 
JaccardMatrix <- comparemodulestwonets(ResultFolder,intModules1,intModules2,
paste('/DenseModuleGene_',indicator1,sep=''),
paste('/DenseModuleGene_',indicator2,sep=''))


[Package MODA version 1.8.0 Index]