Files in GWASTools

Tools for Genome Wide Association Studies

README.md R/hetBySnpSex.R R/Methods-NcdfIntensityReader.R R/gdsSubset.R R/anomStatsPlot.R R/duplicateDiscordanceAcrossDatasets.R R/apartSnpSelection.R R/createAffyIntensityFile.R R/qualityScoreByScan.R R/genotypeToCharacter.R R/assocRegression.R R/findRelationsMeanVar.R R/snpStats.R R/pseudoautoIntensityPlot.R R/hetByScanChrom.R R/pedigreeCheck.R R/meanIntensityByScanChrom.R R/Methods-GdsIntensityReader.R R/batchChisqTest.R R/AllGenerics.R R/anomFilterBAF.R R/Methods-GdsReader.R R/plinkUtils.R R/utils.R R/Methods-GdsGenotypeReader.R R/ibdAreasDraw.R R/simulateGenotypeMatrix.R R/Methods-NcdfGenotypeReader.R R/missingGenotypeByScanChrom.R R/qualityScoreBySnp.R R/Methods-NcdfReader.R R/genoClusterPlot.R R/createDataFile.R R/anomDetectLOH.R R/missingGenotypeBySnpSex.R R/intensityOutliersPlot.R R/meanSdByChromWindow.R R/asVCF.R R/Methods-GenotypeData.R R/checkGenotypeFile.R R/convertNcdfGds.R R/Methods-SnpAnnotationSQLite.R R/checkIntensityFile.R R/imputedDosageFile.R R/findBAFvariance.R R/checkImputedDosageFile.R R/simulateIntensityMatrix.R R/sdByScanChromWindow.R R/pedigreeMaxUnrelated.R R/duplicateDiscordance.R R/BAFfromClusterMeans.R R/chromIntensityPlot.R R/assocCoxPH.R R/anomSegStats.R R/duplicateDiscordanceProbability.R R/Methods-MatrixGenotypeReader.R R/mendelErr.R R/anomDetectBAF.R R/anomIdentifyLowQuality.R R/setMissingGenotypes.R R/qqPlot.R R/exactHWE.R R/vcfWrite.R R/medianSdOverAutosomes.R R/LOHfind.R R/anomSegmentBAF.R R/pedigreePairwiseRelatedness.R R/genoClusterPlotByBatch.R R/AllClasses.R R/gdsSubsetCheck.R R/Methods-ScanAnnotationSQLite.R R/Methods-Iterator.R R/batchFisherTest.R R/createDataUtils.R R/alleleFrequency.R R/manhattanPlot.R R/dupDosageCorAcrossDatasets.R R/snpCorrelationPlot.R R/Methods-IntensityData.R R/ibdPlot.R R/LOHselectAnoms.R R/ibdAssignRelatedness.R R/Methods-SnpAnnotationDataFrame.R R/Methods-ScanAnnotationDataFrame.R R/pedigreeDeleteDuplicates.R R/BAFfromGenotypes.R man/alleleFrequency.Rd man/anomDetectBAF.Rd man/pseudoautosomal.Rd man/duplicateDiscordanceProbability.Rd man/anomSegStats.Rd man/saveas.Rd man/pedigreeMaxUnrelated.Rd man/duplicateDiscordanceAcrossDatasets.Rd man/pedigreePairwiseRelatedness.Rd man/genotypeToCharacter.Rd man/manhattanPlot.Rd man/anomIdentifyLowQuality.Rd man/getobj.Rd man/mendelList.Rd man/GenotypeIterator-class.Rd man/NcdfReader-class.Rd man/GenotypeData-class.Rd man/NcdfGenotypeReader-class.Rd man/hetByScanChrom.Rd man/pedigreeDeleteDuplicates.Rd man/defunct.Rd man/BAFfromClusterMeans.Rd man/readWriteFirst.Rd man/pseudoautoIntensityPlot.Rd man/gdsSubset.Rd man/qualityScoreBySnp.Rd man/createDataFile.Rd man/ScanAnnotationDataFrame-class.Rd man/MatrixGenotypeReader-class.Rd man/assocCoxPH.Rd man/imputedDosageFile.Rd man/SnpAnnotationSQLite-class.Rd man/plinkUtils.Rd man/assocRegression.Rd man/vcfWrite.Rd man/genoClusterPlot.Rd man/allequal.Rd man/HLA.Rd man/qqPlot.Rd man/ScanAnnotationSQLite-class.Rd man/simulateGenotypeMatrix.Rd man/convertNcdfGds.Rd man/missingGenotypeBySnpSex.Rd man/pcaSnpFilters.Rd man/hetBySnpSex.Rd man/exactHWE.Rd man/missingGenotypeByScanChrom.Rd man/GdsReader-class.Rd man/setMissingGenotypes.Rd man/snpCorrelationPlot.Rd man/chromIntensityPlot.Rd man/BAFfromGenotypes.Rd man/GdsGenotypeReader-class.Rd man/snpStats.Rd man/duplicateDiscordance.Rd man/NcdfIntensityReader-class.Rd man/anomDetectLOH.Rd man/apartSnpSelection.Rd man/pedigreeCheck.Rd man/qualityScoreByScan.Rd man/findBAFvariance.Rd man/intensityOutliersPlot.Rd man/relationsMeanVar.Rd man/meanIntensityByScanChrom.Rd man/IntensityData-class.Rd man/pasteSorted.Rd man/getVariable.Rd man/GWASTools-package.Rd man/mendelErr.Rd man/ibdPlot.Rd man/SnpAnnotationDataFrame-class.Rd man/batchTest.Rd man/GdsIntensityReader-class.Rd man/centromeres.Rd tests/test.R inst/doc/Affymetrix.R inst/doc/DataCleaning.pdf inst/doc/Formats.pdf inst/doc/DataCleaning.R inst/doc/Formats.R inst/doc/Affymetrix.pdf inst/unitTests/GdsIntensityReader_test.R inst/unitTests/exactHWE_test.R inst/unitTests/imputedDosageFile_test.R inst/unitTests/findBAFvariance_test.R inst/unitTests/assocRegression_test.R inst/unitTests/batchFisherTest_test.R inst/unitTests/snpStats_test.R inst/unitTests/vcfWrite_test.R inst/unitTests/assocCoxPH_test.R inst/unitTests/plinkUtils_test.R inst/unitTests/missingGenotypeBySnpSex_test.R inst/unitTests/BAFfromClusterMeans_test.R inst/unitTests/SnpAnnotationDataFrame_test.R inst/unitTests/alleleFrequency_test.R inst/unitTests/pedigreePairwiseRelatedness_test.R inst/unitTests/checkIntensityFile_test.R inst/unitTests/ScanAnnotationSQLite_test.R inst/unitTests/IntensityData_test.R inst/unitTests/qualityScoreByScan_test.R inst/unitTests/qualityScoreBySnp_test.R inst/unitTests/Iterator_test.R inst/unitTests/NcdfIntensityReader_test.R inst/unitTests/createAffyIntensityFile_test.R inst/unitTests/apartSnpSelection_test.R inst/unitTests/genotypeToCharacter_test.R inst/unitTests/checkImputedDosageFile_test.R inst/unitTests/gdsSubsetCheck_test.R inst/unitTests/saveas_test.R inst/unitTests/missingGenotypeByScanChrom_test.R inst/unitTests/GenotypeData_test.R inst/unitTests/pseudoautoIntensityPlot_test.R inst/unitTests/gdsSubset_test.R inst/unitTests/hetBySnpSex_test.R inst/unitTests/meanIntensityByScanChrom_test.R inst/unitTests/convertNcdfGds_test.R inst/unitTests/duplicateDiscordance_test.R inst/unitTests/hetByScanChrom_test.R inst/unitTests/ScanAnnotationDataFrame_test.R inst/unitTests/BAFfromGenotypes_test.R inst/unitTests/pedigreeCheck_test.R inst/unitTests/createDataFile_test.R inst/unitTests/SnpAnnotationSQLite_test.R inst/unitTests/pedigreeMaxUnrelated_test.R inst/unitTests/anomDetectBAF_test.R inst/unitTests/dupDosageCorAcrossDatasets_test.R inst/unitTests/batchChisqTest_test.R inst/unitTests/checkGenotypeFile_test.R inst/unitTests/setMissingGenotypes_test.R inst/unitTests/ibdPlot_test.R inst/unitTests/MatrixGenotypeReader_test.R inst/unitTests/GdsReader_test.R inst/unitTests/NcdfGenotypeReader_test.R inst/unitTests/NcdfReader_test.R inst/unitTests/chromIntensityPlot_test.R inst/unitTests/GdsGenotypeReader_test.R inst/unitTests/allequal_test.R inst/unitTests/duplicateDiscordanceAcrossDatasets_test.R inst/unitTests/getobj_test.R inst/unitTests/asVCF_test.R