CompareAllNets {MODA} | R Documentation |
Compare the background network and a set of condition-specific network. Conserved or condition-specific modules are indicated by the plain files, based on the statistics
CompareAllNets(ResultFolder, intModules, indicator, intconditionModules, conditionNames, specificTheta, conservedTheta)
ResultFolder |
where to store results |
intModules |
how many modules in the background network |
indicator |
identifier of current profile, served as a tag in name |
intconditionModules |
a numeric vector, each of them is the number of modules in each condition-specific network. Or just single number |
conditionNames |
a character vector, each of them is the name of condition. Or just single name |
specificTheta |
the threshold to define min(s)+specificTheta, less than which is considered as condition specific module. s is the sums of rows in Jaccard index matrix. See supplementary file. |
conservedTheta |
The threshold to define max(s)-conservedTheta, greater than which is considered as condition conserved module. s is the sums of rows in Jaccard index matrix. See supplementary file. |
None
Dong Li, dxl466@cs.bham.ac.uk
WeightedModulePartitionHierarchical
,
comparemodulestwonets
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 specificTheta = 0.1 #threshold to define condition specific modules conservedTheta = 0.1#threshold to define conserved modules intModules1 <- WeightedModulePartitionHierarchical(datExpr1,ResultFolder, indicator1,CuttingCriterion) intModules2 <- WeightedModulePartitionHierarchical(datExpr2,ResultFolder, indicator2,CuttingCriterion) CompareAllNets(ResultFolder,intModules1,indicator1,intModules2,indicator2, specificTheta,conservedTheta)