comparemodulestwonets: Illustration of two networks comparison

Description Usage Arguments Value Author(s) Examples

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

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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

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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=''))

fairmiracle/MODA documentation built on May 16, 2019, 9:59 a.m.