| BAFfromClusterMeans |
Man page
|
| BAFfromGenotypes |
Man page
|
| GWASTools |
Man page
|
| GWASTools-defunct |
Man page
|
| GWASTools-package |
Man page
|
| GdsGenotypeReader |
Man page
|
| GdsGenotypeReader-class |
Man page
|
| GdsIntensityReader |
Man page
|
| GdsIntensityReader-class |
Man page
|
| GdsReader |
Man page
|
| GdsReader-class |
Man page
|
| GenotypeData |
Man page
|
| GenotypeData-class |
Man page
|
| HLA |
Man page
|
| HLA.hg18 |
Man page
|
| HLA.hg19 |
Man page
|
| HLA.hg38 |
Man page
|
| IntensityData |
Man page
|
| IntensityData-class |
Man page
|
| MatrixGenotypeReader |
Man page
|
| MatrixGenotypeReader-class |
Man page
|
| MchromCode |
Man page
|
| MchromCode,GdsGenotypeReader-method |
Man page
|
| MchromCode,GdsIntensityReader-method |
Man page
|
| MchromCode,GenotypeData-method |
Man page
|
| MchromCode,IntensityData-method |
Man page
|
| MchromCode,MatrixGenotypeReader-method |
Man page
|
| MchromCode,NcdfGenotypeReader-method |
Man page
|
| MchromCode,NcdfIntensityReader-method |
Man page
|
| MchromCode,SnpAnnotationDataFrame-method |
Man page
|
| MchromCode,SnpAnnotationSQLite-method |
Man page
|
| NcdfGenotypeReader |
Man page
|
| NcdfGenotypeReader-class |
Man page
|
| NcdfIntensityReader |
Man page
|
| NcdfIntensityReader-class |
Man page
|
| NcdfReader |
Man page
|
| NcdfReader-class |
Man page
|
| ScanAnnotationDataFrame |
Man page
|
| ScanAnnotationDataFrame-class |
Man page
|
| ScanAnnotationSQLite |
Man page
|
| ScanAnnotationSQLite-class |
Man page
|
| SnpAnnotationDataFrame |
Man page
|
| SnpAnnotationDataFrame-class |
Man page
|
| SnpAnnotationSQLite |
Man page
|
| SnpAnnotationSQLite-class |
Man page
|
| XYchromCode |
Man page
|
| XYchromCode,GdsGenotypeReader-method |
Man page
|
| XYchromCode,GdsIntensityReader-method |
Man page
|
| XYchromCode,GenotypeData-method |
Man page
|
| XYchromCode,IntensityData-method |
Man page
|
| XYchromCode,MatrixGenotypeReader-method |
Man page
|
| XYchromCode,NcdfGenotypeReader-method |
Man page
|
| XYchromCode,NcdfIntensityReader-method |
Man page
|
| XYchromCode,SnpAnnotationDataFrame-method |
Man page
|
| XYchromCode,SnpAnnotationSQLite-method |
Man page
|
| XchromCode |
Man page
|
| XchromCode,GdsGenotypeReader-method |
Man page
|
| XchromCode,GdsIntensityReader-method |
Man page
|
| XchromCode,GenotypeData-method |
Man page
|
| XchromCode,IntensityData-method |
Man page
|
| XchromCode,MatrixGenotypeReader-method |
Man page
|
| XchromCode,NcdfGenotypeReader-method |
Man page
|
| XchromCode,NcdfIntensityReader-method |
Man page
|
| XchromCode,SnpAnnotationDataFrame-method |
Man page
|
| XchromCode,SnpAnnotationSQLite-method |
Man page
|
| YchromCode |
Man page
|
| YchromCode,GdsGenotypeReader-method |
Man page
|
| YchromCode,GdsIntensityReader-method |
Man page
|
| YchromCode,GenotypeData-method |
Man page
|
| YchromCode,IntensityData-method |
Man page
|
| YchromCode,MatrixGenotypeReader-method |
Man page
|
| YchromCode,NcdfGenotypeReader-method |
Man page
|
| YchromCode,NcdfIntensityReader-method |
Man page
|
| YchromCode,SnpAnnotationDataFrame-method |
Man page
|
| YchromCode,SnpAnnotationSQLite-method |
Man page
|
| alleleFrequency |
Man page
|
| allequal |
Man page
|
| anomDetectBAF |
Man page
|
| anomDetectLOH |
Man page
|
| anomFilterBAF |
Man page
|
| anomIdentifyLowQuality |
Man page
|
| anomSegStats |
Man page
|
| anomSegmentBAF |
Man page
|
| anomStatsPlot |
Man page
|
| apartSnpSelection |
Man page
|
| asSnpMatrix |
Man page
|
| assocCoxPH |
Man page
|
| assocRegression |
Man page
|
| assocTestCPH |
Man page
|
| assocTestFisherExact |
Man page
|
| assocTestRegression |
Man page
|
| autosomeCode |
Man page
|
| autosomeCode,GdsGenotypeReader-method |
Man page
|
| autosomeCode,GdsIntensityReader-method |
Man page
|
| autosomeCode,GenotypeData-method |
Man page
|
| autosomeCode,IntensityData-method |
Man page
|
| autosomeCode,MatrixGenotypeReader-method |
Man page
|
| autosomeCode,NcdfGenotypeReader-method |
Man page
|
| autosomeCode,NcdfIntensityReader-method |
Man page
|
| autosomeCode,SnpAnnotationDataFrame-method |
Man page
|
| autosomeCode,SnpAnnotationSQLite-method |
Man page
|
| batchChisqTest |
Man page
|
| batchFisherTest |
Man page
|
| centromeres |
Man page
|
| centromeres.hg18 |
Man page
|
| centromeres.hg19 |
Man page
|
| centromeres.hg38 |
Man page
|
| checkGenotypeFile |
Man page
|
| checkImputedDosageFile |
Man page
|
| checkIntensityFile |
Man page
|
| checkNcdfGds |
Man page
|
| chromIntensityPlot |
Man page
|
| close,GdsReader-method |
Man page
|
| close,GenotypeData-method |
Man page
|
| close,IntensityData-method |
Man page
|
| close,NcdfReader-method |
Man page
|
| close,ScanAnnotationSQLite-method |
Man page
|
| close,SnpAnnotationSQLite-method |
Man page
|
| convertGdsNcdf |
Man page
|
| convertNcdfGds |
Man page
|
| convertVcfGds |
Man page
|
| createAffyIntensityFile |
Man page
|
| createDataFile |
Man page
|
| dupDosageCorAcrossDatasets |
Man page
|
| duplicateDiscordance |
Man page
|
| duplicateDiscordanceAcrossDatasets |
Man page
|
| duplicateDiscordanceProbability |
Man page
|
| exactHWE |
Man page
|
| findBAFvariance |
Man page
|
| gdsCheckImputedDosage |
Man page
|
| gdsImputedDosage |
Man page
|
| gdsSetMissingGenotypes |
Man page
|
| gdsSubset |
Man page
|
| gdsSubsetCheck |
Man page
|
| genoClusterPlot |
Man page
|
| genoClusterPlotByBatch |
Man page
|
| genotypeToCharacter |
Man page
|
| getAlleleA |
Man page
|
| getAlleleA,GdsGenotypeReader-method |
Man page
|
| getAlleleA,GenotypeData-method |
Man page
|
| getAlleleA,SnpAnnotationDataFrame-method |
Man page
|
| getAlleleA,SnpAnnotationSQLite-method |
Man page
|
| getAlleleB |
Man page
|
| getAlleleB,GdsGenotypeReader-method |
Man page
|
| getAlleleB,GenotypeData-method |
Man page
|
| getAlleleB,SnpAnnotationDataFrame-method |
Man page
|
| getAlleleB,SnpAnnotationSQLite-method |
Man page
|
| getAnnotation |
Man page
|
| getAnnotation,ScanAnnotationDataFrame-method |
Man page
|
| getAnnotation,ScanAnnotationSQLite-method |
Man page
|
| getAnnotation,SnpAnnotationDataFrame-method |
Man page
|
| getAnnotation,SnpAnnotationSQLite-method |
Man page
|
| getAttribute |
Man page
|
| getAttribute,GdsReader-method |
Man page
|
| getAttribute,NcdfReader-method |
Man page
|
| getBAlleleFreq |
Man page
|
| getBAlleleFreq,GdsIntensityReader-method |
Man page
|
| getBAlleleFreq,IntensityData-method |
Man page
|
| getBAlleleFreq,NcdfIntensityReader-method |
Man page
|
| getChromosome |
Man page
|
| getChromosome,GdsGenotypeReader-method |
Man page
|
| getChromosome,GdsIntensityReader-method |
Man page
|
| getChromosome,GenotypeData-method |
Man page
|
| getChromosome,IntensityData-method |
Man page
|
| getChromosome,MatrixGenotypeReader-method |
Man page
|
| getChromosome,NcdfGenotypeReader-method |
Man page
|
| getChromosome,NcdfIntensityReader-method |
Man page
|
| getChromosome,SnpAnnotationDataFrame-method |
Man page
|
| getChromosome,SnpAnnotationSQLite-method |
Man page
|
| getDimension |
Man page
|
| getDimension,GdsReader-method |
Man page
|
| getDimension,NcdfReader-method |
Man page
|
| getDimensionNames |
Man page
|
| getDimensionNames,NcdfReader-method |
Man page
|
| getGenotype |
Man page
|
| getGenotype,GdsGenotypeReader-method |
Man page
|
| getGenotype,GenotypeData-method |
Man page
|
| getGenotype,MatrixGenotypeReader-method |
Man page
|
| getGenotype,NcdfGenotypeReader-method |
Man page
|
| getGenotypeSelection |
Man page
|
| getGenotypeSelection,GdsGenotypeReader-method |
Man page
|
| getGenotypeSelection,GenotypeData-method |
Man page
|
| getGenotypeSelection,MatrixGenotypeReader-method |
Man page
|
| getLogRRatio |
Man page
|
| getLogRRatio,GdsIntensityReader-method |
Man page
|
| getLogRRatio,IntensityData-method |
Man page
|
| getLogRRatio,NcdfIntensityReader-method |
Man page
|
| getMetadata |
Man page
|
| getMetadata,ScanAnnotationDataFrame-method |
Man page
|
| getMetadata,ScanAnnotationSQLite-method |
Man page
|
| getMetadata,SnpAnnotationDataFrame-method |
Man page
|
| getMetadata,SnpAnnotationSQLite-method |
Man page
|
| getNodeDescription |
Man page
|
| getNodeDescription,GdsReader-method |
Man page
|
| getPosition |
Man page
|
| getPosition,GdsGenotypeReader-method |
Man page
|
| getPosition,GdsIntensityReader-method |
Man page
|
| getPosition,GenotypeData-method |
Man page
|
| getPosition,IntensityData-method |
Man page
|
| getPosition,MatrixGenotypeReader-method |
Man page
|
| getPosition,NcdfGenotypeReader-method |
Man page
|
| getPosition,NcdfIntensityReader-method |
Man page
|
| getPosition,SnpAnnotationDataFrame-method |
Man page
|
| getPosition,SnpAnnotationSQLite-method |
Man page
|
| getQuality |
Man page
|
| getQuality,GdsIntensityReader-method |
Man page
|
| getQuality,IntensityData-method |
Man page
|
| getQuality,NcdfIntensityReader-method |
Man page
|
| getQuery |
Man page
|
| getQuery,ScanAnnotationSQLite-method |
Man page
|
| getQuery,SnpAnnotationSQLite-method |
Man page
|
| getScanAnnotation |
Man page
|
| getScanAnnotation,GenotypeData-method |
Man page
|
| getScanID |
Man page
|
| getScanID,GdsGenotypeReader-method |
Man page
|
| getScanID,GdsIntensityReader-method |
Man page
|
| getScanID,GenotypeData-method |
Man page
|
| getScanID,IntensityData-method |
Man page
|
| getScanID,MatrixGenotypeReader-method |
Man page
|
| getScanID,NcdfGenotypeReader-method |
Man page
|
| getScanID,NcdfIntensityReader-method |
Man page
|
| getScanID,ScanAnnotationDataFrame-method |
Man page
|
| getScanID,ScanAnnotationSQLite-method |
Man page
|
| getScanVariable |
Man page
|
| getScanVariable,GenotypeData-method |
Man page
|
| getScanVariable,IntensityData-method |
Man page
|
| getScanVariableNames |
Man page
|
| getScanVariableNames,GenotypeData-method |
Man page
|
| getScanVariableNames,IntensityData-method |
Man page
|
| getSex |
Man page
|
| getSex,GenotypeData-method |
Man page
|
| getSex,IntensityData-method |
Man page
|
| getSex,ScanAnnotationDataFrame-method |
Man page
|
| getSex,ScanAnnotationSQLite-method |
Man page
|
| getSnpAnnotation |
Man page
|
| getSnpAnnotation,GenotypeData-method |
Man page
|
| getSnpID |
Man page
|
| getSnpID,GdsGenotypeReader-method |
Man page
|
| getSnpID,GdsIntensityReader-method |
Man page
|
| getSnpID,GenotypeData-method |
Man page
|
| getSnpID,IntensityData-method |
Man page
|
| getSnpID,MatrixGenotypeReader-method |
Man page
|
| getSnpID,NcdfGenotypeReader-method |
Man page
|
| getSnpID,NcdfIntensityReader-method |
Man page
|
| getSnpID,SnpAnnotationDataFrame-method |
Man page
|
| getSnpID,SnpAnnotationSQLite-method |
Man page
|
| getSnpVariable |
Man page
|
| getSnpVariable,GenotypeData-method |
Man page
|
| getSnpVariable,IntensityData-method |
Man page
|
| getSnpVariableNames |
Man page
|
| getSnpVariableNames,GenotypeData-method |
Man page
|
| getSnpVariableNames,IntensityData-method |
Man page
|
| getVariable |
Man page
|
| getVariable,GdsGenotypeReader-method |
Man page
|
| getVariable,GdsIntensityReader-method |
Man page
|
| getVariable,GdsReader-method |
Man page
|
| getVariable,GenotypeData-method |
Man page
|
| getVariable,IntensityData-method |
Man page
|
| getVariable,NcdfGenotypeReader-method |
Man page
|
| getVariable,NcdfIntensityReader-method |
Man page
|
| getVariable,NcdfReader-method |
Man page
|
| getVariable,ScanAnnotationDataFrame-method |
Man page
|
| getVariable,ScanAnnotationSQLite-method |
Man page
|
| getVariable,SnpAnnotationDataFrame-method |
Man page
|
| getVariable,SnpAnnotationSQLite-method |
Man page
|
| getVariableNames |
Man page
|
| getVariableNames,GdsReader-method |
Man page
|
| getVariableNames,NcdfReader-method |
Man page
|
| getVariableNames,ScanAnnotationDataFrame-method |
Man page
|
| getVariableNames,ScanAnnotationSQLite-method |
Man page
|
| getVariableNames,SnpAnnotationDataFrame-method |
Man page
|
| getVariableNames,SnpAnnotationSQLite-method |
Man page
|
| getX |
Man page
|
| getX,GdsIntensityReader-method |
Man page
|
| getX,IntensityData-method |
Man page
|
| getX,NcdfIntensityReader-method |
Man page
|
| getY |
Man page
|
| getY,GdsIntensityReader-method |
Man page
|
| getY,IntensityData-method |
Man page
|
| getY,NcdfIntensityReader-method |
Man page
|
| getobj |
Man page
|
| gwasExactHW |
Man page
|
| hasBAlleleFreq |
Man page
|
| hasBAlleleFreq,GdsIntensityReader-method |
Man page
|
| hasBAlleleFreq,IntensityData-method |
Man page
|
| hasBAlleleFreq,NcdfIntensityReader-method |
Man page
|
| hasCoordVariable |
Man page
|
| hasCoordVariable,NcdfReader-method |
Man page
|
| hasLogRRatio |
Man page
|
| hasLogRRatio,GdsIntensityReader-method |
Man page
|
| hasLogRRatio,IntensityData-method |
Man page
|
| hasLogRRatio,NcdfIntensityReader-method |
Man page
|
| hasQuality |
Man page
|
| hasQuality,GdsIntensityReader-method |
Man page
|
| hasQuality,IntensityData-method |
Man page
|
| hasQuality,NcdfIntensityReader-method |
Man page
|
| hasScanAnnotation |
Man page
|
| hasScanAnnotation,GenotypeData-method |
Man page
|
| hasScanAnnotation,IntensityData-method |
Man page
|
| hasScanVariable |
Man page
|
| hasScanVariable,GenotypeData-method |
Man page
|
| hasScanVariable,IntensityData-method |
Man page
|
| hasSex |
Man page
|
| hasSex,GenotypeData-method |
Man page
|
| hasSex,IntensityData-method |
Man page
|
| hasSex,ScanAnnotationDataFrame-method |
Man page
|
| hasSex,ScanAnnotationSQLite-method |
Man page
|
| hasSnpAnnotation |
Man page
|
| hasSnpAnnotation,GenotypeData-method |
Man page
|
| hasSnpAnnotation,IntensityData-method |
Man page
|
| hasSnpVariable |
Man page
|
| hasSnpVariable,GenotypeData-method |
Man page
|
| hasSnpVariable,IntensityData-method |
Man page
|
| hasVariable |
Man page
|
| hasVariable,GdsReader-method |
Man page
|
| hasVariable,GenotypeData-method |
Man page
|
| hasVariable,IntensityData-method |
Man page
|
| hasVariable,NcdfReader-method |
Man page
|
| hasVariable,ScanAnnotationDataFrame-method |
Man page
|
| hasVariable,ScanAnnotationSQLite-method |
Man page
|
| hasVariable,SnpAnnotationDataFrame-method |
Man page
|
| hasVariable,SnpAnnotationSQLite-method |
Man page
|
| hasX |
Man page
|
| hasX,GdsIntensityReader-method |
Man page
|
| hasX,IntensityData-method |
Man page
|
| hasX,NcdfIntensityReader-method |
Man page
|
| hasY |
Man page
|
| hasY,GdsIntensityReader-method |
Man page
|
| hasY,IntensityData-method |
Man page
|
| hasY,NcdfIntensityReader-method |
Man page
|
| hetByScanChrom |
Man page
|
| hetBySnpSex |
Man page
|
| ibdAreasDraw |
Man page
|
| ibdAssignRelatedness |
Man page
|
| ibdAssignRelatednessKing |
Man page
|
| ibdPlot |
Man page
|
| imputedDosageFile |
Man page
|
| intensityOutliersPlot |
Man page
|
| kingIBS0FSCI |
Man page
|
| manhattanPlot |
Man page
|
| meanIntensityByScanChrom |
Man page
|
| meanSdByChromWindow |
Man page
|
| medianSdOverAutosomes |
Man page
|
| mendelErr |
Man page
|
| mendelList |
Man page
|
| mendelListAsDataFrame |
Man page
|
| minorAlleleDetectionAccuracy |
Man page
|
| missingGenotypeByScanChrom |
Man page
|
| missingGenotypeBySnpSex |
Man page
|
| ncdfAddData |
Man page
|
| ncdfAddIntensity |
Man page
|
| ncdfCheckGenotype |
Man page
|
| ncdfCheckIntensity |
Man page
|
| ncdfCreate |
Man page
|
| ncdfImputedDosage |
Man page
|
| ncdfSetMissingGenotypes |
Man page
|
| ncdfSubset |
Man page
|
| ncdfSubsetCheck |
Man page
|
| nscan |
Man page
|
| nscan,GdsGenotypeReader-method |
Man page
|
| nscan,GdsIntensityReader-method |
Man page
|
| nscan,GenotypeData-method |
Man page
|
| nscan,IntensityData-method |
Man page
|
| nscan,MatrixGenotypeReader-method |
Man page
|
| nscan,NcdfGenotypeReader-method |
Man page
|
| nscan,NcdfIntensityReader-method |
Man page
|
| nscan,ScanAnnotationSQLite-method |
Man page
|
| nsnp |
Man page
|
| nsnp,GdsGenotypeReader-method |
Man page
|
| nsnp,GdsIntensityReader-method |
Man page
|
| nsnp,GenotypeData-method |
Man page
|
| nsnp,IntensityData-method |
Man page
|
| nsnp,MatrixGenotypeReader-method |
Man page
|
| nsnp,NcdfGenotypeReader-method |
Man page
|
| nsnp,NcdfIntensityReader-method |
Man page
|
| nsnp,SnpAnnotationSQLite-method |
Man page
|
| open,GdsReader-method |
Man page
|
| open,GenotypeData-method |
Man page
|
| open,IntensityData-method |
Man page
|
| open,NcdfReader-method |
Man page
|
| open,ScanAnnotationSQLite-method |
Man page
|
| open,SnpAnnotationSQLite-method |
Man page
|
| pasteSorted |
Man page
|
| pcaSnpFilters |
Man page
|
| pcaSnpFilters.hg18 |
Man page
|
| pcaSnpFilters.hg19 |
Man page
|
| pcaSnpFilters.hg38 |
Man page
|
| pedigreeCheck |
Man page
|
| pedigreeDeleteDuplicates |
Man page
|
| pedigreeMaxUnrelated |
Man page
|
| pedigreePairwiseRelatedness |
Man page
|
| plinkCheck |
Man page
|
| plinkToNcdf |
Man page
|
| plinkWrite |
Man page
|
| pseudoautoIntensityPlot |
Man page
|
| pseudoautosomal |
Man page
|
| pseudoautosomal.hg18 |
Man page
|
| pseudoautosomal.hg19 |
Man page
|
| pseudoautosomal.hg38 |
Man page
|
| qqPlot |
Man page
|
| qualityScoreByScan |
Man page
|
| qualityScoreBySnp |
Man page
|
| readWriteFirst |
Man page
|
| relationsMeanVar |
Man page
|
| saveas |
Man page
|
| sdByScanChromWindow |
Man page
|
| setMissingGenotypes |
Man page
|
| show,GdsReader-method |
Man page
|
| show,GenotypeData-method |
Man page
|
| show,IntensityData-method |
Man page
|
| show,MatrixGenotypeReader-method |
Man page
|
| show,NcdfReader-method |
Man page
|
| show,ScanAnnotationSQLite-method |
Man page
|
| show,SnpAnnotationSQLite-method |
Man page
|
| simulateGenotypeMatrix |
Man page
|
| simulateIntensityMatrix |
Man page
|
| snpCorrelationPlot |
Man page
|
| vcfCheck |
Man page
|
| vcfWrite |
Man page
|
| writeAnnotation |
Man page
|
| writeAnnotation,ScanAnnotationSQLite-method |
Man page
|
| writeAnnotation,SnpAnnotationSQLite-method |
Man page
|
| writeMetadata |
Man page
|
| writeMetadata,ScanAnnotationSQLite-method |
Man page
|
| writeMetadata,SnpAnnotationSQLite-method |
Man page
|
