analyze-config1.json

{ 
  "bm2FileName" : "/analysis/myfile.bm2",
  "jsonExportFileName" : "/analysis/myfile.json",
  "overwrite" : true,
  "expressionDataConfigs" : [ {
    "inputFileName" : "/analysis/data/",
    "hasHeaders" : false,
    "logTransformation" : "BASE2",
    "platform" : "GPL1355"
  }
  ],
  "preFilterConfigs" : [ {
    "@type" : "anova",
    "pValueCutoff" : 0.05,
    "useMultipleTestingCorrection" : false,
    "filterOutControlGenes" : true,
    "useFoldChange" : true,
    "foldChange" : 2.0,
    "foldChangeLotel" : 1.5,
    "pValueLotel" : 0.05,
    "lotelTest" : 2,   
    "numberOfThreads" : 4
  }, {
    "@type" : "williams",
    "pValueCutoff" : 0.05,
    "useMultipleTestingCorrection" : false,
    "filterOutControlGenes" : true,
    "useFoldChange" : true,
    "numberOfPermutations": 50,
    "foldChange" : 2.0,
    "foldChangeLotel" : 1.5,
    "pValueLotel" : 0.05,
    "lotelTest" : 2,   
    "numberOfThreads" : 4
  } ],
  "bmdsConfigs" : [ {
    "modelConfigs" : [ {
      "@type" : "hill"
    }, {
      "@type" : "power"
    }, {
      "@type" : "poly",
      "degree" : 1
    }, {
      "@type" : "poly",
      "degree" : 2
    }, {
      "@type" : "exp",
      "expModel" : 3
    }],
    "bmdsBestModelSelection" : {
      "bestPolyTest" : 1,
      "pValueCutoff" : 0.05,
      "flagHillWithKParameter" : true,
      "kParameterValue" : 1,
      "bestModelSelectionWithFlaggedHill" : 1,
      "modifyFlaggedHillWithFractionMinBMD" : 0.05
    },
    "bmdsInputConfig" : {
      "maxIterations" : 250,
      "confidenceLevel" : 0.95,
      "constantVariance" : true,
      "restrictPower" : true,
      "bmrFactor" : 1.349
    },
    "inputCategory" : "williams",
    "numberOfThreads" : 100
  }, {
    "modelConfigs" : [ {
      "@type" : "hill"
    }, {
      "@type" : "power"
    }, {
      "@type" : "poly",
      "degree" : 1
    }, {
      "@type" : "poly",
      "degree" : 2
    }, {
      "@type" : "poly",
      "degree" : 3
    }, {
      "@type" : "exp",
      "expModel" : 2
    }, {
      "@type" : "exp",
      "expModel" : 3
    }, {
      "@type" : "exp",
      "expModel" : 4
    }, {
      "@type" : "exp",
      "expModel" : 5
    } ],
    "bmdsBestModelSelection" : {
      "bestPolyTest" : 1,
      "pValueCutoff" : 0.05,
      "flagHillWithKParameter" : true,
      "kParameterValue" : 1,
      "bestModelSelectionWithFlaggedHill" : 1,
      "modifyFlaggedHillWithFractionMinBMD" : 0.05
    },
    "bmdsInputConfig" : {
      "maxIterations" : 250,
      "confidenceLevel" : 0.95,
      "constantVariance" : true,
      "restrictPower" : true,
      "bmrFactor" : 1.349
    },
    "inputCategory" : "anova",
    "numberOfThreads" : 100
  } ],
  "categoryAnalysisConfigs" : [ {
    "@type" : "go",
    "removePromiscuousProbes" : true,
    "removeBMDGreaterHighDose" : true,
    "bmdPValueCutoff" : 0.1,
    "bmdBMDLRatioMin" : null,
    "bmduBMDRatioMin" : null,
    "bmduBMDLRatioMin" : 20.0,
    "nFoldBelowLowestDose" : 10.0,
    "identifyConflictingProbeSets" : null,
    "correlationCutoffForConflictingProbeSets" : null,
    "goCategory" : "universal"
  }, {
    "@type" : "pathway",
    "removePromiscuousProbes" : true,
    "removeBMDGreaterHighDose" : true,
    "bmdPValueCutoff" : 0.1,
    "bmdBMDLRatioMin" : null,
    "bmduBMDRatioMin" : null,
    "bmduBMDLRatioMin" : 20.0,
    "nFoldBelowLowestDose" : 10.0,
    "identifyConflictingProbeSets" : null,
    "correlationCutoffForConflictingProbeSets" : null,
    "signalingPathway" : "REACTOME"
  }, {
    "@type" : "defined",
    "removePromiscuousProbes" : true,
    "removeBMDGreaterHighDose" : true,
    "bmdPValueCutoff" : 0.1,
    "bmdBMDLRatioMin" : null,
    "bmduBMDRatioMin" : null,
    "bmduBMDLRatioMin" : 20.0,
    "nFoldBelowLowestDose" : 10.0,
    "identifyConflictingProbeSets" : null,
    "correlationCutoffForConflictingProbeSets" : null,
    "probeFilePath" : "/analysis/defined/probes.txt",
    "categoryFilePath" : "/analysis/defined/categories.txt"
  }]
}