comparemodulestwonets: Illustration of two networks comparison

In MODA: MODA: MOdule Differential Analysis for weighted gene co-expression network

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, [e-mail]

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=''))

MODA documentation built on Nov. 8, 2020, 6:39 p.m.