CompareAllNets: Illustration of network comparison
In MODA: MODA: MOdule Differential Analysis for weighted gene co-expression network

Description Usage Arguments Value Author(s) See Also Examples

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

1 2	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)