d31b598ad489e65fc33ccd15f40b8fd3 *DESCRIPTION
08758e948f8fd6da2a8cf92ab036b105 *NAMESPACE
881fa0bd1e2652357fdd1f4174737fd7 *R/AddIDsToVertices.r
a5a9fef67772ceaafd84a0e2a14062b4 *R/AddWeightsToEdges.r
c5b3dc349b6918d724bbfc96577375fa *R/AnalyseExperimentalData.r
07fa560a8f0707f3f2dc973ad6864d48 *R/AnalysePredictionsList.r
4f872f8727d3b7d32da045ae0b9f7d70 *R/CalculateEnrichmentPValue.r
77885b798bbed0fe50675e1604fdde52 *R/CalculateSignificance.r
fec562c7a018f8194717ed7f08a18bd3 *R/CalculateSignificanceUsingCubicAlgorithm.r
f3b7130705907ae1d9a014e861b198a8 *R/CalculateSignificanceUsingCubicAlgorithm1b.r
a9419c4e37f8c5d6427a25fd57e10d0f *R/CalculateSignificanceUsingQuarticAlgorithm.r
a1077503f9dd50f779f97a774aa097a8 *R/CalculateTotalWeightForAllContingencyTables.r
8a3952ea8e8f011b53393d909d2c7c7b *R/CalculateWeightGivenValuesInThreeByThreeContingencyTable.r
95f53935589809163b5d8dec0fa1c14f *R/CausalR-package.r
a6c4cea7cac0f546ff757485700cb050 *R/CheckPossibleValuesAreValid.r
06a34504b2e7757c957d360a6c266501 *R/CheckRowAndColumnSumValuesAreValid.r
63b52514cc956d4d9b44557db943e77e *R/CompareHypothesis.r
f406db9779c72a4bcf2c4510e043f6f9 *R/ComputeFinalDistribution.r
3f0e1296ab0b1a5c8588043c688080f8 *R/ComputePValueFromDistributionTable.r
0ddfdd4b6c629f9ebc998ae62a63a25b *R/CreateCCG.r
9f535e68c6f3918ed4748edf32904360 *R/CreateCG.r
91bf21f214ebc806d4d70a4a9e84dd77 *R/CreateNetworkFromTable.r
f66f01a6d1625940f044ca3862a2dd58 *R/DetermineInteractionTypeOfPath.r
5f0fcc299f9b6ecdd670bdedb0cb47fd *R/FindApproximateValuesThatWillMaximiseDValue.r
cc93f5e29cd12f1015283fe788b43cd6 *R/FindIdsOfConnectedNodesInSubgraph.r
fdb0b9a6d3ed618f5b74f2daa6217e2f *R/FindMaximumDValue.r
5b30b60ce1817bc8cf6e28aa88675029 *R/GetAllPossibleRoundingCombinations.r
42d47af7649792f25d4871993375dbf3 *R/GetApproximateMaximumDValueFromThreeByTwoContingencyTable.r
23e10b19d808ec2efec54557b2e4744f *R/GetApproximateMaximumDValueFromTwoByTwoContingencyTable.r
d8c78cee773030d362be1f44c0d66fa7 *R/GetCombinationsOfCorrectandIncorrectPredictions.r
61cff2136203fc7a60a1b68a735dfbfd *R/GetExplainedNodesOfCCG.r
50ba380c2ef01fe9764558b9418982da *R/GetInteractionInformation.r
fbc36c587645681cf72f97f93181dc6a *R/GetMatrixOfCausalRelationships.r
a9d089f73ad6e685bf29598261a1b188 *R/GetMaxDValueForAFamily.r
4df968abf49f4955222e15c52d2a5297 *R/GetMaxDValueForAThreeByTwoFamily.r
755ca88ef3efe655e9e07daf85c731af *R/GetMaximumDValueFromTwoByTwoContingencyTable.r
2c65511bd8066ab308a8303429b8be02 *R/GetNodeID.r
53415c42ffecfd511874c21220507f42 *R/GetNodeName.r
cdeb2dbbe82f110df43e885c117ae082 *R/GetNumberOfPositiveAndNegativeEntries.r
442d406b9c8468fd4082f29944ff6f2d *R/GetPathsInSifFormat.r
d8e1d80ae5c14f0fb154d398d83507a8 *R/GetRegulatedNodes.r
e4f4f2b2826ccf1c31c684d1be36dd0a *R/GetRowAndColumnSumValues.r
656af1234cd3d4052eaeaa2abb3d4b81 *R/GetScoreForNumbersOfCorrectandIncorrectPredictions.r
bba8c40921d05fc6922cadd721f00d76 *R/GetScoresForSingleNode.r
d9446a53e21fe4ca56282f33268109b6 *R/GetScoresWeightsMatrix.r
a68189df0e0beb9a1559ab1e4cfa1a8e *R/GetScoresWeightsMatrixByCubicAlg.r
e65bc7d8a0ccc98fa5dd1915bd2fdf25 *R/GetSetOfDifferentiallyExpressedGenes.r
675019d24428d0e110020d9bb0fdcbb4 *R/GetSetOfSignificantPredictions.r
58e49c14c38a76852158984fc52f658c *R/GetShortestPathsFromCCG.r
3ac9bb2d8267bfe122dc07357d0b8ba9 *R/GetWeightForNumbersOfCorrectandIncorrectPredictions.r
5d878811e2fc85d091c063f2e49dd093 *R/GetWeightsAboveHypothesisScoreAndTotalWeights.r
9218f6a333cd1e15d7618cacb763c417 *R/GetWeightsAboveHypothesisScoreForAThreeByTwoTable.r
94c58502a89abf306cdbe51afe930ae9 *R/GetWeightsFromInteractionInformation.r
534b9be42cd61365380966b87cde1fe3 *R/MakePredictions.r
87f78eac87acdd25f5c57e612ab79c6b *R/MakePredictionsFromCCG.r
db03600c3c13a76e616f6d18ce54e689 *R/MakePredictionsFromCG.r
3b4c4f1d5ca3b8e47ab7d4f7f5d28350 *R/OrderHypotheses.r
8116bb7b0d07749f0844069fb603fec5 *R/PlotGraphWithNodeNames.r
aa1affb915c33aa6c3e8876767baedeb *R/PopulateTheThreeByThreeContingencyTable.r
2bf1317b85f9f556d545f385e70480e9 *R/PopulateTwoByTwoContingencyTable.r
0b5be982e7f03c13590d0815ba88253c *R/ProcessExperimentalData.r
2e6f889aebd03fb32ec6e1f11a74354c *R/RankTheHypotheses.r
a5e51ee91a977b9aaadc4a6fdbc566e9 *R/ReadExperimentalData.r
069271315cbe5b25070984748f258419 *R/ReadSifFileToTable.r
aa7762d7ccdb8cab707e2decaebdf253 *R/RemoveIDsNotInExperimentalData.r
84301ff844c2444245bf6f9557a0471a *R/ScoreHypothesis.r
39c9c4f18ca6f14fc32235f5daf84467 *R/ValidateFormatOfDataTable.r
5b8096ad05dc7a3104d0956609abaca4 *R/ValidateFormatOfTable.r
0bb6fee777504fa01cb3ae4cc06c2849 *R/WriteAllExplainedNodesToSifFile.r
b31e59d702b80bd4b982fb59311c09da *R/WriteExplainedNodesToSifFile.r
8b6b33e724bd66308d0f70fbc52960d4 *R/runRankHypothesis.r
21c7692c67b9c777438a4b0962af0357 *R/runSCANR.r
0143f46aff8c028310b1f56f70112c04 *build/vignette.rds
e42020f33bbd159351f63c56fe235937 *inst/doc/CausalR.R
1b42871242a55e5ab95f19a414e8698e *inst/doc/CausalR.pdf
d25e999e4973f96c3bec90f95bb8a7a9 *inst/doc/CausalR.rnw
d0c4d2301234bafb36c5ada77a8f88da *inst/extdata/testData.txt
5aa80e0e5bc1159c049304ee9aade184 *inst/extdata/testData1.txt
4164dc49f6ad3051c6a1719ca775c6ac *inst/extdata/testNetwork.sif
a3452071c00c0afea656573a57f76602 *inst/extdata/testNetwork1.sif
34ba6c40f4d189fc99b88eea72d43077 *inst/testData/CCGWithTwoLevels.txt
8298393b0899876e589e05349667c3a9 *inst/testData/network_with_conflict.sif
a560534fa5030bf2338d965592ff160a *inst/testData/network_with_difflength_conflict.sif
6d6cd90f38a2c10d5ea28e2742e9e249 *inst/testData/network_with_loop.sif
4b090fddaad7c4df93b2ba0e9d276956 *inst/testData/test_ExperimentalData.txt
f4896b64aedcde1b431e8e7452a3db8a *inst/testData/test_network.sif
34ba6c40f4d189fc99b88eea72d43077 *inst/unitTests/CCGWithTwoLevels.txt
bbab07316af07bc18ff8bb6cca94ade3 *inst/unitTests/CheckEdgeForTest_SifFileReader.r
b1d65b9bf20fa30896b1a12306d3a124 *inst/unitTests/CreateCGForTest_RankTheHypotheses.r
f9565791ec9773760c03702fe9a78a90 *inst/unitTests/CreateInteractionInfoTableForTest_SifFileReader.r
ffbf2af792e669e99609056f4672a9a7 *inst/unitTests/CreateNetworkForTest_SifFileReader.r
123c67a8afb825b021a9864f60e10fd2 *inst/unitTests/CreateSimpleNetworkForTest_ComputationalCausalGraphCreator.r
007075b99e70b66bef0fad805707fa39 *inst/unitTests/CreateTestTableForTest_SifFileReader.r
8f2c55d9f885e12400a6474b92a2e86d *inst/unitTests/DetermineInteractionTypeOfPath.r
51ac92a1439355520e9e7a9e026ea4e7 *inst/unitTests/GetMatrixOfCausalRelationships.r
e7731f8d68313dcfff95a601831ce04c *inst/unitTests/RemoveIDsNotInExperimentalData.r
8298393b0899876e589e05349667c3a9 *inst/unitTests/network_with_conflict.sif
a560534fa5030bf2338d965592ff160a *inst/unitTests/network_with_difflength_conflict.sif
6d6cd90f38a2c10d5ea28e2742e9e249 *inst/unitTests/network_with_loop.sif
de42cd056886cb0cbc12c8ac76e307aa *inst/unitTests/test_CausalReasoningPredictions.R
ec5880a18a5dcd9adde6544197a2ed51 *inst/unitTests/test_CubicAlgorithm.R
48331a4b2428088bc8716c280ca71c4c *inst/unitTests/test_CubicAlgorithm1b.R
de3b2fb36d06202de15a5536de671be2 *inst/unitTests/test_EnrichmentPValueCalculation.R
4b090fddaad7c4df93b2ba0e9d276956 *inst/unitTests/test_ExperimentalData.txt
f42e69deb018fdb44fcb75161f145a11 *inst/unitTests/test_ExperimentalDataReader.R
7c77c3e9fe79949ae368cd11d2ce2a71 *inst/unitTests/test_HypothesisScorer.R
906ee2fc04f414d125db71aa0f1bc75b *inst/unitTests/test_InputNodes.txt
022897eb86432e7f37be347b33452a38 *inst/unitTests/test_NodeInclusionFile.txt
be16cdee1cf02a44b44505e2c1ff5efb *inst/unitTests/test_QuarticAlgorithm.R
ecefa26f7be645f06429b17e7d248f52 *inst/unitTests/test_RankTheHypotheses.R
f3a5353f55ec75c577eb0924d8c8cf54 *inst/unitTests/test_SifFileReader.R
b7ef184bc3fda30c1eda36c9353258d2 *inst/unitTests/test_SignificanceCalculator.R
202353c19c4305c7893412836c6b3875 *inst/unitTests/test_WriteExplainedNodesToSifFile.R
f4896b64aedcde1b431e8e7452a3db8a *inst/unitTests/test_network.sif
8e5554249f82cb63dd7180bbc4df3590 *man/AddIDsToVertices.Rd
8e779cbfc5b75e605740a79967d39da0 *man/AddWeightsToEdges.Rd
c3b028de14e27bbc52f256d4c47aed93 *man/AnalyseExperimentalData.Rd
33d6ca76a37a71b3881678a997efa48d *man/AnalysePredictionsList.Rd
61937ea3cbf02fc3cb438e809f7203e1 *man/CalculateEnrichmentPValue.Rd
22f816deb103023a3437a874254e5a68 *man/CalculateSignificance.Rd
7652613cd5aaf3d9c4a76378a811f433 *man/CalculateSignificanceUsingCubicAlgorithm.Rd
cef1996691d7ea489ed5b08c1eeee8df *man/CalculateSignificanceUsingCubicAlgorithm1b.Rd
46eeb2d6bd0a4870175565fcd804c6db *man/CalculateSignificanceUsingQuarticAlgorithm.Rd
3955134ca2f107d3967761d85454878f *man/CalculateTotalWeightForAllContingencyTables.Rd
f8ccea0db8d9ed89b3f109cd0e48093b *man/CalculateWeightGivenValuesInThreeByThreeContingencyTable.Rd
b749afffe83390f9834d32fdcc281ae7 *man/CausalR-package.Rd
1007e3dccbdaed6ba19e5340ee68c925 *man/CheckPossibleValuesAreValid.Rd
3b260dfec19940e93c460d5a765be484 *man/CheckRowAndColumnSumValuesAreValid.Rd
4edfe3ddcef26f7508c4a2af61ff7191 *man/CompareHypothesis.Rd
f3b2f4a327bd89048b1bd6541d6b870d *man/ComputeFinalDistribution.Rd
b565b9074718a98e706ceddf61b6e0a4 *man/ComputePValueFromDistributionTable.Rd
a200800f922c92b7a0cd380533d02517 *man/CreateCCG.Rd
06fd4458986531d214fb9ad5bc320c63 *man/CreateCG.Rd
75e18fc7ec459ea7fc79fba0f0c1b01a *man/CreateNetworkFromTable.Rd
e2e617c03acfeb9fd4418eeefc02a02c *man/DetermineInteractionTypeOfPath.Rd
5c6905573f0196735b4b22116b5a4357 *man/FindApproximateValuesThatWillMaximiseDValue.Rd
9ba66e5dd1fbaec4d25b3de7632487c3 *man/FindIdsOfConnectedNodesInSubgraph.Rd
dae7750321d4a5a9e47942bcdd5562dd *man/FindMaximumDValue.Rd
28b60b706d0404fca4fff3006edcbc89 *man/GetAllPossibleRoundingCombinations.Rd
0f254781b0b8b8c38e4af3eb097cd8d9 *man/GetApproximateMaximumDValueFromThreeByTwoContingencyTable.Rd
27fb74156eb909fa185b58b222b39d1d *man/GetApproximateMaximumDValueFromTwoByTwoContingencyTable.Rd
6338f9d4347514d8a15768ceeb5ed2af *man/GetCombinationsOfCorrectandIncorrectPredictions.Rd
2e343bc57d5bb70ef051bd72e20dc802 *man/GetExplainedNodesOfCCG.Rd
53d3f592a49bcb3d8cde428e2d7833a5 *man/GetInteractionInformation.Rd
847d61b76483d92fd54dc8e3fc0269b6 *man/GetMatrixOfCausalRelationships.Rd
81063d74ee957dce4d533f9822574f10 *man/GetMaxDValueForAFamily.Rd
c70397e3bf0048baefd5abe431b6d792 *man/GetMaxDValueForAThreeByTwoFamily.Rd
e269d7cd6bdcad5088c0b71de88c0e2b *man/GetMaximumDValueFromTwoByTwoContingencyTable.Rd
145ef61afdc736b41c4af4a6472c5191 *man/GetNodeID.Rd
b0460fb839bd3709990fee03e64e6f93 *man/GetNodeName.Rd
93bc8e6f8de2a0db29470758d8e5f925 *man/GetNumberOfPositiveAndNegativeEntries.Rd
49c4c3a10c630b330ab0e5f09c826a58 *man/GetPathsInSifFormat.Rd
144df742ab4f94c71f02c761a0cb0a13 *man/GetRegulatedNodes.Rd
0054853b8626f62ab1857b6b32230fa1 *man/GetRowAndColumnSumValues.Rd
4ab43175788458a67e8a9d24d392927f *man/GetScoreForNumbersOfCorrectandIncorrectPredictions.Rd
f55c00ddc7d873472b061d1da7dfbfef *man/GetScoresForSingleNode.Rd
e7052f5f8ec9326e8d2be80800d3945c *man/GetScoresWeightsMatrix.Rd
9de05a4f4dbe824980785cf560a4ac94 *man/GetScoresWeightsMatrixByCubicAlg.Rd
b6665a9293427b613a07782538d88915 *man/GetSetOfDifferentiallyExpressedGenes.Rd
e7289b3cc6b4e5a657b0dc71847d54e5 *man/GetSetOfSignificantPredictions.Rd
5969eec563d9326e41fa6e8c859260e5 *man/GetShortestPathsFromCCG.Rd
19417d27dc7a698126afa6fd42d8e9cd *man/GetWeightForNumbersOfCorrectandIncorrectPredictions.Rd
4fe5e82d55d841a095fdcfddafc2842d *man/GetWeightsAboveHypothesisScoreAndTotalWeights.Rd
2ab844563928a676d935cd6d25d5e47d *man/GetWeightsAboveHypothesisScoreForAThreeByTwoTable.Rd
ce5950dafc09d57b57a95a13ed220381 *man/GetWeightsFromInteractionInformation.Rd
2987c990257748dfd4abcc699a69c3c4 *man/MakePredictions.Rd
b49f08db90526be281ee82c1afad92a3 *man/MakePredictionsFromCCG.Rd
40c1a629f9557933798cf0e9021d3623 *man/MakePredictionsFromCG.Rd
5ec2cc2116d9c165bc7c5aded4a426cb *man/OrderHypotheses.Rd
268496e1cf3dea5f2564647ec42dc07c *man/PlotGraphWithNodeNames.Rd
4c2939a1863c10486dffd04d11d3e487 *man/PopulateTheThreeByThreeContingencyTable.Rd
59852ac0823ebe11a199246a13c66d55 *man/PopulateTwoByTwoContingencyTable.Rd
63895cfb8fc9efa1b41ea49629b8ca0b *man/ProcessExperimentalData.Rd
f009dd25872f08b141a32ecc7c5e526c *man/RankTheHypotheses.Rd
3799beaa723d9c66b6a2c230f4902014 *man/ReadExperimentalData.Rd
b87cf364b127726f2d7dd81f16a7bc51 *man/ReadSifFileToTable.Rd
32b25b86fdb8feb307092d7a45f63a37 *man/RemoveIDsNotInExperimentalData.Rd
d21d6472823c4d1a6faf0e0cc049a4ac *man/ScoreHypothesis.Rd
ca06cb27ffa4f8d0726498589dc8772c *man/ValidateFormatOfDataTable.Rd
f775df94544f733f9314e0f5eca262b0 *man/ValidateFormatOfTable.Rd
49b85caf6ba04df2ba7afb3134f97c15 *man/WriteAllExplainedNodesToSifFile.Rd
c5364349d3f7252418ff7ca5e78ff49d *man/WriteExplainedNodesToSifFile.Rd
e2fde7c5941c28445ea27064919de252 *man/runRankHypothesis.Rd
16e94045afd3ef220243f68efcb6a01b *man/runSCANR.Rd
230a8787c2307f8ac0428a2bb646a67b *tests/runTests.R
d25e999e4973f96c3bec90f95bb8a7a9 *vignettes/CausalR.rnw
aca36c4e56d3163f64b4e3ace857c745 *vignettes/DifferentialData.txt
becd3d2be1fbd6ed3d8fb6993e5fcf2a *vignettes/Fig1.png
ce50834e59c850c0fba247d477b4ae7e *vignettes/Fig2.png
c4b4f58795abc742398555b1fd8bfc5d *vignettes/Fig3.png
feed87b7b2a5de9b7783da5941b548f5 *vignettes/Fig4.png
27a07b0f8b7c1cda6c7f7136a5cd1dfc *vignettes/figure/unnamed-chunk-4-1.pdf
4eb6044bdf545afc4fc24168ec1c2c29 *vignettes/figure/unnamed-chunk-6-1.pdf
