comparemodulestwonets {MODA} | R Documentation |
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.
comparemodulestwonets(sourcehead, nm1, nm2, ind1, ind2)
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 |
A matrix where each entry is the Jaccard index of corresponding modules from two networks
Dong Li, dxl466@cs.bham.ac.uk
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=''))