Man pages for Genentech/MiDAS
R package for immunogenomics data handling and association analysis

aaVariationToCountsTransform amino acid variation data frame into counts table
adjustPValuesAdjust P-values for Multiple Comparisons
allele_frequenciesAlleles frequencies scraped from allelefrequencies.net
analyzeAssociationsAssociation analysis
analyzeConditionalAssociationsStepwise conditional association analysis
applyInheritanceModelApply inheritance model
as.data.frame.MiDASCoerce MiDAS to Data Frame
backquoteBackquote character
characterMatchesCheck if character matches one of possible values
checkAlleleFormatCheck HLA allele format
checkColDataFormatAssert colData data
checkHlaCallsFormatAssert hla calls data frame format
checkKirCallsFormatAssert KIR counts data frame format
checkKirGenesFormatCheck KIR genes format
checkStatisticalModelAssert statistical model
colnamesMatchesCheck column names
convertAlleleToVariableConvert allele numbers to additional variables
countsToVariablesConvert counts table to variables
dfToExperimentMatHelper transform data frame to experiment matrix
dict_dist_granthamGrantham distance
distGranthamCalculate Grantham distance between amino acid sequences
experimentMatToDfHelper transform experiment matrix to data frame
filterByFrequencyFilter MiDAS object by frequency
filterByOmnibusGroupsFilter MiDAS object by omnibus groups
filterByVariablesFilter MiDAS object by features
filterExperimentByFrequencyFilter experiment by frequency
filterExperimentByVariablesFilter experiment by variable
filterListByElementsFilter list by elements
formatResultsPretty format statistical analysis results helper
getAAFrequenciesCalculate amino acid frequencies
getAlleleResolutionInfer HLA allele resolution
getAllelesForAAGet HLA alleles for amino acid position
getExperimentFrequenciesCalculate experiment's features frequencies
getExperimentPopulationMultiplicatorGet experiment's population multiplicator
getExperimentsGet available experiments in MiDAS object.
getFrequenciesCalculate features frequencies for a given experiment in...
getFrequencyMaskHelper function for filtering frequency data frame
getHlaCallsGet HLA calls from MiDAS object.
getHlaCallsGenesGet HLA calls genes
getHlaFrequenciesCalculate HLA allele frequencies
getHlaKirInteractionsGet HLA - KIR interactions
getKirCallsGet KIR calls from MiDAS object.
getKIRFrequenciesCalculate KIR genes frequencies
getObjectDetailsGet attributes of statistical model object
getOmnibusGroupsGet omnibus groups from MiDAS object.
getPlaceholderGet placeholder name from MiDAS object.
getReferenceFrequenciesHelper transforming reference frequencies
getVariableAAPosFind variable positions in sequence alignment
hasTidyMethodCheck if tidy method for class exist
hlaAlignmentGranthamHelper function returning alignment for Grantham distance...
hlaCallsGranthamDistanceCalculate Grantham distance between HLA alleles
hlaCallsToCountsTransform HLA calls to counts table
hlaToAAVariationGenerate amino acid variation matrix
hlaToVariableConvert HLA calls to variables
HWETestTest for Hardy Weinberg equilibrium
isCharacterOrNULLCheck if object is character vector or NULL
isClassCheck if object is of class x
isClassOrNULLCheck if object is of class x or null
isCountOrNULLCheck if object is count or NULL
isCountsOrZerosCheck if vector contains only counts or zeros
isExperimentCountsOrZerosCheck if frequencies can be calculated for an experiment
isExperimentInheritanceModelApplicableCheck if experiment is inheritance model applicable
isFlagOrNULLCheck if object is flag or NULL
isNumberOrNULLCheck if object is number or NULL
isStringOrNULLCheck if object is string or NULL
isTRUEorFALSECheck if object is TRUE or FALSE flag
iterativeLRTIterative likelihood ratio test
iterativeModelIteratively evaluate model for different variables
kableResultsCreate association analysis results table in HTML or LaTeX
kir_frequenciesKIR genes frequencies scraped from allelefrequencies.net
lapply_tryCatchlapply with tryCatch routine
listMiDASDictionariesList HLA alleles dictionaries
LRTestLikelihood ratio test
MiDAS-classMiDAS class
midasToWideTransform MiDAS to wide format data.frame
MiDAS_tut_HLAMiDAS tutorial HLA data
MiDAS_tut_KIRMiDAS tutorial KIR data
MiDAS_tut_objectMiDAS tutorial MiDAS object
MiDAS_tut_phenoMiDAS tutorial phenotype data
objectHasPlaceholderCheck if placeholder is present in object formula
omnibusTestOmnibus test
prepareMiDASConstruct a MiDAS object
prepareMiDAS_hla_aaPrepare MiDAS data on HLA amino acid level
prepareMiDAS_hla_allelesPrepare MiDAS data on HLA allele level
prepareMiDAS_hla_customPrepare MiDAS data on custom HLA level
prepareMiDAS_hla_divergencePrepare MiDAS data on HLA divergence level
prepareMiDAS_hla_g_groupsPrepare MiDAS data on HLA allele's G groups level
prepareMiDAS_hla_hetPrepare MiDAS data on HLA heterozygosity level
prepareMiDAS_hla_kir_interactionsPrepare MiDAS data on HLA - KIR interactions level
prepareMiDAS_hla_NK_ligandsPrepare MiDAS data on HLA allele's groups level
prepareMiDAS_hla_supertypesPrepare MiDAS data on HLA allele's supertypes level
prepareMiDAS_kir_customPrepare MiDAS data on custom KIR level
prepareMiDAS_kir_genesPrepare MiDAS data on KIR genes level
prepareMiDAS_kir_haplotypesPrepare MiDAS data on KIR haplotypes level
readHlaAlignmentsRead HLA allele alignments
readHlaCallsRead HLA allele calls
readKirCallsRead KIR calls
reduceAlleleResolutionReduce HLA alleles
reduceHlaCallsReduce HLA calls resolution
runMiDASRun MiDAS statistical analysis
runMiDASGetVarsFreqGet variables frequencies from MiDAS
stringMatchesCheck if string matches one of possible values
summariseAAPositionSummarize amino acid position
updateModelExtend and Re-fit a Model Call
validateFrequencyCutoffsValidate frequency cutoffs
Genentech/MiDAS documentation built on Feb. 5, 2024, 11:52 a.m.