API for UW-GAC/GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

Global functions
.addNames Source code
.addWindows Source code
.alleleFreq Source code
.averageGroupVar Source code
.calcAIcovMats Source code
.calcAIcovMatsResids Source code
.calcAIhetvars Source code
.calcISAFBeta Source code
.calcISAFBetaPCProd Source code
.calcLikelihoodQuantities Source code
.calcPvalVCTest Source code
.calcWorkingYnonGaussian Source code
.calc_cmp_pval Source code
.checkCovMatSampleId Source code
.checkFamily Source code
.checkMatrixType Source code
.checkNullModelTestSingle Source code
.checkRownames Source code
.checkXSampleId Source code
.computeSigmaQuantities Source code
.covMatNames Source code
.covMatSubset Source code
.createPCMatrix Source code
.estISAF Source code
.estListToDT Source code
.fastG Source code
.fastH Source code
.filterMonomorphic Source code
.fitNullModel Source code
.genoAsMatrix Source code
.genoDataToGds Source code
.indexList Source code
.iterateAIREMLworkingY Source code
.kingToMatrix Source code
.listIdentical Source code
.makeSparseMatrix_df Source code
.makeSparseMatrix_matrix Source code
.matListCombine Source code
.match.arg Source code
.matchAlleles Source code
.meanImputeFn Source code
.modelCovarString Source code
.modelMatrixColumns Source code
.modelOutcomeString Source code
.modelString Source code
.muBoundaryFilt Source code
.muBoundaryTrunc Source code
.nullModOutMM Source code
.nullModOutReg Source code
.nullModOutWLS Source code
.nullModelAsMatrix Source code
.pcair Source code
.pcairPartitionUser Source code
.pchisqsum Source code
.pcrCalcIBDOvr Source code
.pcrCalcIBDVar Source code
.pcrCalcKinNone Source code
.pcrCalcKinOvr Source code
.pcrCalcKinVar Source code
.pcrCalcNone Source code
.pcrCalcOvr Source code
.pcrCalcVar Source code
.pcrelate Source code
.pcrelateCalcRatio Source code
.pcrelateChecks Source code
.pcrelateToMatrix Source code
.pcrelateVarBlock Source code
.poibinP Source code
.prepGenoBlock Source code
.rankNorm Source code
.readKing Source code
.regular Source code
.runAIREMLgaussian Source code
.runAIREMLother Source code
.sampleIndexNullModel Source code
.setCovMatNames Source code
.setFilterNullModel Source code
.stopOnError Source code
.testGenoBlockAggregate Source code
.testGenoBlockSingle Source code
.testGenoSingleVarBR Source code
.testGenoSingleVarCMP Source code
.testGenoSingleVarScore Source code
.testGenoSingleVarWaldGxE Source code
.testSingleVarMultAlleles Source code
.testVariantSetBurden Source code
.testVariantSetSKAT Source code
.testVariantSetSKATO Source code
.testVariantSetSMMAT Source code
.updateNullModelFormat Source code
.weightFromFreq Source code
GENESIS Man page
GENESIS-defunct Man page
GENESIS-package Man page
HapMap_ASW_MXL_KINGmat Man page
SPA_pval Source code
admixMap Man page Source code
admixMapMM Man page
assocTestAggregate Man page
assocTestAggregate,GenotypeIterator-method Man page
assocTestAggregate,SeqVarIterator-method Man page
assocTestAggregate-methods Man page
assocTestMM Man page
assocTestSeq Man page
assocTestSeqWindow Man page
assocTestSingle Man page
assocTestSingle,GenotypeIterator-method Man page
assocTestSingle,SeqVarIterator-method Man page
assocTestSingle-methods Man page
calcGtilde Source code
calcGtildeFast Source code
calcISAFBeta Man page Source code
calcScore Man page Source code
computeVSIF Man page Source code
computeVSIFNullModel Man page Source code
correctK0 Man page Source code
correctK2 Man page Source code
correctKin Man page Source code
createDesignMatrix Source code
effectAllele Man page
effectAllele,GenotypeData-method Man page
effectAllele,SeqVarGDSClass-method Man page
effectAllele-methods Man page
expit Source code
fitNullMM Man page
fitNullModel Man page
fitNullModel,AnnotatedDataFrame-method Man page
fitNullModel,GenotypeData-method Man page
fitNullModel,ScanAnnotationDataFrame-method Man page
fitNullModel,SeqVarData-method Man page
fitNullModel,data.frame-method Man page
fitNullModel-methods Man page
fitNullModelFastScore Man page
fitNullModelFastScore,SeqVarData-method Man page
fitNullModelFastScore-methods Man page
fitNullReg Man page
integrateFxn Source code
isNullModelFastScore Man page Source code
isNullModelSmall Man page Source code
jointScoreTest Man page Source code
kin2gds Man page Source code
king2mat Man page
kingToMatrix Man page
kingToMatrix,character-method Man page
kingToMatrix,snpgdsIBDClass-method Man page
makeSparseMatrix Man page
makeSparseMatrix,Matrix-method Man page
makeSparseMatrix,data.frame-method Man page
makeSparseMatrix,data.table-method Man page
makeSparseMatrix,matrix-method Man page
makeSparseMatrix-methods Man page
mat2gds Man page Source code
nullModelFastScore Man page Source code
nullModelInvNorm Man page Source code
nullModelSmall Man page Source code
nullModelSubset Source code
nullModelTestPrep Source code
pcair Man page
pcair,GdsGenotypeReader-method Man page
pcair,GenotypeData-method Man page
pcair,MatrixGenotypeReader-method Man page
pcair,SNPGDSFileClass-method Man page
pcair,SeqVarGDSClass-method Man page
pcair,gds.class-method Man page
pcair-methods Man page
pcairPartition Man page Source code
pchisqsum_rsvd Source code
pchisqsum_ssvd Source code
pcrelate Man page
pcrelate,GenotypeData-method Man page
pcrelate,GenotypeIterator-method Man page
pcrelate,SeqVarData-method Man page
pcrelate,SeqVarIterator-method Man page
pcrelateMakeGRM Man page
pcrelateReadInbreed Man page
pcrelateReadKinship Man page
pcrelateSampBlock Man page Source code
pcrelateToMatrix Man page
pcrelateToMatrix,pcrelate-method Man page
plot.pcair Man page Source code
print.pcair Man page Source code
print.summary.pcair Man page Source code
sample_annotation_1KG Man page
samplesGdsOrder Man page Source code
skatO_qchisqsum Source code
srfht Source code
srfht2 Source code
subsetCholSigmaInv Source code
summary.pcair Man page Source code
testGenoSingleVar Source code
testSingleVarianceComponent Source code
testVariantSet Source code
tracefht Source code
updateNullModCond Source code
varCompCI Man page Source code
UW-GAC/GENESIS documentation built on June 14, 2022, 3:05 p.m.