aaVariationToCounts	aaVariationToCounts
adjustPValues	adjustPValues
allele_frequencies	allele_frequencies
analyzeAssociations	analyzeAssociations
analyzeConditionalAssociations	analyzeConditionalAssociations
applyInheritanceModel	applyInheritanceModel
applyInheritanceModel.matrix	applyInheritanceModel
applyInheritanceModel.SummarizedExperiment	applyInheritanceModel
as.data.frame.MiDAS	as.data.frame.MiDAS
backquote	backquote
characterMatches	characterMatches
checkAlleleFormat	checkAlleleFormat
checkColDataFormat	checkColDataFormat
checkHlaCallsFormat	checkHlaCallsFormat
checkKirCallsFormat	checkKirCallsFormat
checkKirGenesFormat	checkKirGenesFormat
checkStatisticalModel	checkStatisticalModel
colnamesMatches	colnamesMatches
convertAlleleToVariable	convertAlleleToVariable
countsToVariables	countsToVariables
dfToExperimentMat	dfToExperimentMat
dict_dist_grantham	dict_dist_grantham
distGrantham	distGrantham
experimentMatToDf	experimentMatToDf
filterByFrequency	filterByFrequency
filterByFrequency,MiDAS-method	MiDAS-class
filterByOmnibusGroups	filterByOmnibusGroups
filterByOmnibusGroups,MiDAS-method	MiDAS-class
filterByVariables	filterByVariables
filterByVariables,MiDAS-method	MiDAS-class
filterExperimentByFrequency	filterExperimentByFrequency
filterExperimentByFrequency.matrix	filterExperimentByFrequency
filterExperimentByFrequency.SummarizedExperiment	filterExperimentByFrequency
filterExperimentByVariables	filterExperimentByVariables
filterExperimentByVariables.matrix	filterExperimentByVariables
filterExperimentByVariables.SummarizedExperiment	filterExperimentByVariables
filterListByElements	filterListByElements
formatResults	formatResults
getAAFrequencies	getAAFrequencies
getAlleleResolution	getAlleleResolution
getAllelesForAA	getAllelesForAA
getAllelesForAA,MiDAS-method	MiDAS-class
getExperimentFrequencies	getExperimentFrequencies
getExperimentFrequencies.matrix	getExperimentFrequencies
getExperimentFrequencies.SummarizedExperiment	getExperimentFrequencies
getExperimentPopulationMultiplicator	getExperimentPopulationMultiplicator
getExperimentPopulationMultiplicator.matrix	getExperimentPopulationMultiplicator
getExperimentPopulationMultiplicator.SummarizedExperiment	getExperimentPopulationMultiplicator
getExperiments	getExperiments
getExperiments,MiDAS-method	MiDAS-class
getFrequencies	getFrequencies
getFrequencies,MiDAS-method	MiDAS-class
getFrequencyMask	getFrequencyMask
getHlaCalls	getHlaCalls
getHlaCalls,MiDAS-method	MiDAS-class
getHlaCallsGenes	getHlaCallsGenes
getHlaFrequencies	getHlaFrequencies
getHlaKirInteractions	getHlaKirInteractions
getKirCalls	getKirCalls
getKirCalls,MiDAS-method	MiDAS-class
getKIRFrequencies	getKIRFrequencies
getObjectDetails	getObjectDetails
getOmnibusGroups	getOmnibusGroups
getOmnibusGroups,MiDAS-method	MiDAS-class
getPlaceholder	getPlaceholder
getPlaceholder,MiDAS-method	MiDAS-class
getReferenceFrequencies	getReferenceFrequencies
getVariableAAPos	getVariableAAPos
hasTidyMethod	hasTidyMethod
hlaAlignmentGrantham	hlaAlignmentGrantham
hlaCallsGranthamDistance	hlaCallsGranthamDistance
hlaCallsToCounts	hlaCallsToCounts
hlaToAAVariation	hlaToAAVariation
hlaToVariable	hlaToVariable
HWETest	HWETest
isCharacterOrNULL	isCharacterOrNULL
isClass	isClass
isClassOrNULL	isClassOrNULL
isCountOrNULL	isCountOrNULL
isCountsOrZeros	isCountsOrZeros
isExperimentCountsOrZeros	isExperimentCountsOrZeros
isExperimentInheritanceModelApplicable	isExperimentInheritanceModelApplicable
isExperimentInheritanceModelApplicable.matrix	isExperimentInheritanceModelApplicable
isExperimentInheritanceModelApplicable.SummarizedExperiment	isExperimentInheritanceModelApplicable
isFlagOrNULL	isFlagOrNULL
isNumberOrNULL	isNumberOrNULL
isStringOrNULL	isStringOrNULL
isTRUEorFALSE	isTRUEorFALSE
iterativeLRT	iterativeLRT
iterativeModel	iterativeModel
kableResults	kableResults
kir_frequencies	kir_frequencies
lapply_tryCatch	lapply_tryCatch
listMiDASDictionaries	listMiDASDictionaries
LRTest	LRTest
MiDAS	MiDAS-class
MiDAS-class	MiDAS-class
midasToWide	midasToWide
MiDAS_tut_HLA	MiDAS_tut_HLA
MiDAS_tut_KIR	MiDAS_tut_KIR
MiDAS_tut_object	MiDAS_tut_object
MiDAS_tut_pheno	MiDAS_tut_pheno
objectHasPlaceholder	objectHasPlaceholder
omnibusTest	omnibusTest
prepareMiDAS	prepareMiDAS
prepareMiDAS_hla_aa	prepareMiDAS_hla_aa
prepareMiDAS_hla_alleles	prepareMiDAS_hla_alleles
prepareMiDAS_hla_custom	prepareMiDAS_hla_custom
prepareMiDAS_hla_divergence	prepareMiDAS_hla_divergence
prepareMiDAS_hla_g_groups	prepareMiDAS_hla_g_groups
prepareMiDAS_hla_het	prepareMiDAS_hla_het
prepareMiDAS_hla_kir_interactions	prepareMiDAS_hla_kir_interactions
prepareMiDAS_hla_NK_ligands	prepareMiDAS_hla_NK_ligands
prepareMiDAS_hla_supertypes	prepareMiDAS_hla_supertypes
prepareMiDAS_kir_custom	prepareMiDAS_kir_custom
prepareMiDAS_kir_genes	prepareMiDAS_kir_genes
prepareMiDAS_kir_haplotypes	prepareMiDAS_kir_haplotypes
readHlaAlignments	readHlaAlignments
readHlaCalls	readHlaCalls
readKirCalls	readKirCalls
reduceAlleleResolution	reduceAlleleResolution
reduceHlaCalls	reduceHlaCalls
runMiDAS	runMiDAS
runMiDASGetVarsFreq	runMiDASGetVarsFreq
stringMatches	stringMatches
summariseAAPosition	summariseAAPosition
updateModel	updateModel
validateFrequencyCutoffs	validateFrequencyCutoffs
