modulePreservation: modulePreservation
In milescsmith/WGCNA: Weighted Correlation Network Analysis

modulePreservation

R Documentation

modulePreservation

Description

modulePreservation

Usage

modulePreservation(
  multiData,
  multiColor,
  dataIsExpr = TRUE,
  networkType = "unsigned",
  corFnc = "cor",
  corOptions = "use = 'p'",
  referenceNetworks = 1,
  testNetworks = NULL,
  nPermutations = 100,
  includekMEallInSummary = FALSE,
  restrictSummaryForGeneralNetworks = TRUE,
  calculateQvalue = FALSE,
  randomSeed = 12345,
  maxGoldModuleSize = 1000,
  maxModuleSize = 1000,
  quickCor = 1,
  ccTupletSize = 2,
  calculateCor.kIMall = FALSE,
  calculateClusterCoeff = FALSE,
  useInterpolation = FALSE,
  checkData = TRUE,
  greyName = NULL,
  savePermutedStatistics = TRUE,
  loadPermutedStatistics = FALSE,
  permutedStatisticsFile = if (useInterpolation) "permutedStats-intrModules.RData" else
    "permutedStats-actualModules.RData",
  plotInterpolation = TRUE,
  interpolationPlotFile = "modulePreservationInterpolationPlots.pdf",
  discardInvalidOutput = TRUE,
  parallelCalculation = FALSE,
  verbose = 1,
  indent = 0
)

Arguments

`multiData`
`multiColor`
`dataIsExpr`
`networkType`
`corFnc`
`corOptions`
`referenceNetworks`
`testNetworks`
`nPermutations`
`includekMEallInSummary`
`restrictSummaryForGeneralNetworks`
`calculateQvalue`
`randomSeed`
`maxGoldModuleSize`
`maxModuleSize`
`quickCor`
`ccTupletSize`
`calculateCor.kIMall`
`calculateClusterCoeff`
`useInterpolation`
`checkData`
`greyName`
`savePermutedStatistics`
`loadPermutedStatistics`
`permutedStatisticsFile`
`plotInterpolation`
`interpolationPlotFile`
`discardInvalidOutput`
`parallelCalculation`
`verbose`
`indent`