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
GENESIS Man page
GENESIS-defunct Man page
GENESIS-deprecated Man page
GENESIS-package Man page
HapMap_ASW_MXL_KINGmat Man page
XchromCode Source code
YchromCode Source code
addNames Source code
addWindows Source code
admixMap Man page Source code
admixMapMM Man page Source code
alleleFreq Source code Source code
apply Source code
apply.Matrix Source code
apply.gds.class Source code
apply.matrix Source code
assocTestAggregate Man page
assocTestAggregate,GenotypeIterator-method Man page
assocTestAggregate,SeqVarIterator-method Man page
assocTestAggregate-methods Man page
assocTestMM Man page Source code
assocTestSeq Man page Source code
assocTestSeqWindow Man page Source code
assocTestSingle Man page
assocTestSingle,GenotypeIterator-method Man page
assocTestSingle,SeqVarIterator-method Man page
assocTestSingle-methods Man page
averageGroupVar Source code
calcAIcovMats Source code
calcAIcovMatsResids Source code
calcAIhetvars Source code
calcLikelihoodQuantities Source code
calcPval Source code
calcWorkingYnonGaussian Source code
calcXtilde Source code
checkMatrixType Source code
checkRownames Source code
checkSampleId Source code
computeSigmaQuantities Source code
covMatNames Source code
covMatSubset Source code
createDesignMatrix Source code
createDesignMatrix1 Source code
estISAF Source code
fitNullMM Man page Source code
fitNullModel Man page Source code
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
fitNullReg Man page Source code
genoAsMatrix Source code
getBlocks Source code
getScanIndex Source code
getSnpIndex Source code
hasSex Source code
integrateFxn Source code
kin2gds Man page Source code
king2mat Man page Source code
kingToMatrix Man page Source code
mat2gds Man page Source code
matchAlleles Source code
meanImpute Source code
modelMatrixColumns Source code
ndexList Source code
nullModOutMM Source code
nullModOutReg Source code
nullModOutWLS Source code
nullModelAsMatrix Source code
nullModelInvNorm Man page Source code
nullModelSubset Source code
nullModelTestPrep Source code
pcair Man page Source code
pcair,GdsGenotypeReader-method Man page
pcair,GenotypeData-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
pcrelate Man page Source code
pcrelateMakeGRM Man page Source code
pcrelateReadInbreed Man page Source code
pcrelateReadKinship Man page Source code
plot.pcair Man page Source code
poibinMidp Source code
prepareGenotype Source code
print.pcair Man page Source code
print.summary.pcair Man page Source code
rankNorm Source code
readSampleId Source code
readSampleId.Matrix Source code
readSampleId.gds.class Source code
readSampleId.matrix Source code
runAIREMLgaussian Source code
runAIREMLgaussian1 Source code
runAIREMLother Source code
runAIREMLother1 Source code
runSKATTest Source code
runWLSgaussian Source code
sample_annotation_1KG Man page
setFilterNullModel Source code
skatO_qchisqsum Source code
subsetCholSigmaInv Source code
summary.pcair Man page Source code
terateAIREMLworkingY Source code
testGenoSingleVar Source code
testGenoSingleVarBR Source code
testGenoSingleVarScore Source code
testGenoSingleVarWald Source code
testGenoSingleVarWaldGxE Source code
testSingleVarMultAlleles Source code
testSingleVarianceComponent Source code
testVariantSet Source code
testVariantSetBurden Source code
testVariantSetSKAT Source code
testVariantSetSMMAT Source code
updateNullModCond Source code
updateNullModOutcome Source code
varCompCI Man page Source code
weightFromFreq Source code
UW-GAC/GENESIS documentation built on Oct. 17, 2018, 5:31 a.m.