CompareAllNets {MODA}R Documentation

Illustration of network comparison

Description

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

Usage

CompareAllNets(ResultFolder, intModules, indicator, intconditionModules,
  conditionNames, specificTheta, conservedTheta)

Arguments

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.

Value

None

Author(s)

Dong Li, dxl466@cs.bham.ac.uk

See Also

WeightedModulePartitionHierarchical, comparemodulestwonets

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
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)


[Package MODA version 1.10.0 Index]