HWETest                 Test for Hardy Weinberg equilibrium
LRTest                  Likelihood ratio test
MiDAS-class             MiDAS class
MiDAS_tut_HLA           MiDAS tutorial HLA data
MiDAS_tut_KIR           MiDAS tutorial KIR data
MiDAS_tut_object        MiDAS tutorial MiDAS object
MiDAS_tut_pheno         MiDAS tutorial phenotype data
aaVariationToCounts     Transform amino acid variation data frame into
                        counts table
adjustPValues           Adjust P-values for Multiple Comparisons
allele_frequencies      Alleles frequencies scraped from
                        allelefrequencies.net
analyzeAssociations     Association analysis
analyzeConditionalAssociations
                        Stepwise conditional association analysis
applyInheritanceModel   Apply inheritance model
as.data.frame.MiDAS     Coerce MiDAS to Data Frame
backquote               Backquote character
characterMatches        Check if character matches one of possible
                        values
checkAlleleFormat       Check HLA allele format
checkColDataFormat      Assert colData data
checkHlaCallsFormat     Assert hla calls data frame format
checkKirCallsFormat     Assert KIR counts data frame format
checkKirGenesFormat     Check KIR genes format
checkStatisticalModel   Assert statistical model
colnamesMatches         Check column names
convertAlleleToVariable
                        Convert allele numbers to additional variables
countsToVariables       Convert counts table to variables
dfToExperimentMat       Helper transform data frame to experiment
                        matrix
dict_dist_grantham      Grantham distance
distGrantham            Calculate Grantham distance between amino acid
                        sequences
experimentMatToDf       Helper transform experiment matrix to data
                        frame
filterByFrequency       Filter MiDAS object by frequency
filterByOmnibusGroups   Filter MiDAS object by omnibus groups
filterByVariables       Filter MiDAS object by features
filterExperimentByFrequency
                        Filter experiment by frequency
filterExperimentByVariables
                        Filter experiment by variable
filterListByElements    Filter list by elements
formatResults           Pretty format statistical analysis results
                        helper
getAAFrequencies        Calculate amino acid frequencies
getAlleleResolution     Infer HLA allele resolution
getAllelesForAA         Get HLA alleles for amino acid position
getExperimentFrequencies
                        Calculate experiment's features frequencies
getExperimentPopulationMultiplicator
                        Get experiment's population multiplicator
getExperiments          Get available experiments in MiDAS object.
getFrequencies          Calculate features frequencies for a given
                        experiment in MiDAS object.
getFrequencyMask        Helper function for filtering frequency data
                        frame
getHlaCalls             Get HLA calls from MiDAS object.
getHlaCallsGenes        Get HLA calls genes
getHlaFrequencies       Calculate HLA allele frequencies
getHlaKirInteractions   Get HLA - KIR interactions
getKIRFrequencies       Calculate KIR genes frequencies
getKirCalls             Get KIR calls from MiDAS object.
getObjectDetails        Get attributes of statistical model object
getOmnibusGroups        Get omnibus groups from MiDAS object.
getPlaceholder          Get placeholder name from MiDAS object.
getReferenceFrequencies
                        Helper transforming reference frequencies
getVariableAAPos        Find variable positions in sequence alignment
hasTidyMethod           Check if tidy method for class exist
hlaAlignmentGrantham    Helper function returning alignment for
                        Grantham distance calculations
hlaCallsGranthamDistance
                        Calculate Grantham distance between HLA alleles
hlaCallsToCounts        Transform HLA calls to counts table
hlaToAAVariation        Generate amino acid variation matrix
hlaToVariable           Convert HLA calls to variables
isCharacterOrNULL       Check if object is character vector or NULL
isClass                 Check if object is of class x
isClassOrNULL           Check if object is of class x or null
isCountOrNULL           Check if object is count or NULL
isCountsOrZeros         Check if vector contains only counts or zeros
isExperimentCountsOrZeros
                        Check if frequencies can be calculated for an
                        experiment
isExperimentInheritanceModelApplicable
                        Check if experiment is inheritance model
                        applicable
isFlagOrNULL            Check if object is flag or NULL
isNumberOrNULL          Check if object is number or NULL
isStringOrNULL          Check if object is string or NULL
isTRUEorFALSE           Check if object is TRUE or FALSE flag
iterativeLRT            Iterative likelihood ratio test
iterativeModel          Iteratively evaluate model for different
                        variables
kableResults            Create association analysis results table in
                        HTML or LaTeX
kir_frequencies         KIR genes frequencies scraped from
                        allelefrequencies.net
lapply_tryCatch         lapply with tryCatch routine
listMiDASDictionaries   List HLA alleles dictionaries
midasToWide             Transform MiDAS to wide format data.frame
objectHasPlaceholder    Check if placeholder is present in object
                        formula
omnibusTest             Omnibus test
prepareMiDAS            Construct a MiDAS object
prepareMiDAS_hla_NK_ligands
                        Prepare MiDAS data on HLA allele's groups level
prepareMiDAS_hla_aa     Prepare MiDAS data on HLA amino acid level
prepareMiDAS_hla_alleles
                        Prepare MiDAS data on HLA allele level
prepareMiDAS_hla_custom
                        Prepare MiDAS data on custom HLA level
prepareMiDAS_hla_divergence
                        Prepare MiDAS data on HLA divergence level
prepareMiDAS_hla_g_groups
                        Prepare MiDAS data on HLA allele's G groups
                        level
prepareMiDAS_hla_het    Prepare MiDAS data on HLA heterozygosity level
prepareMiDAS_hla_kir_interactions
                        Prepare MiDAS data on HLA - KIR interactions
                        level
prepareMiDAS_hla_supertypes
                        Prepare MiDAS data on HLA allele's supertypes
                        level
prepareMiDAS_kir_custom
                        Prepare MiDAS data on custom KIR level
prepareMiDAS_kir_genes
                        Prepare MiDAS data on KIR genes level
prepareMiDAS_kir_haplotypes
                        Prepare MiDAS data on KIR haplotypes level
readHlaAlignments       Read HLA allele alignments
readHlaCalls            Read HLA allele calls
readKirCalls            Read KIR calls
reduceAlleleResolution
                        Reduce HLA alleles
reduceHlaCalls          Reduce HLA calls resolution
runMiDAS                Run MiDAS statistical analysis
runMiDASGetVarsFreq     Get variables frequencies from MiDAS
stringMatches           Check if string matches one of possible values
summariseAAPosition     Summarize amino acid position
updateModel             Extend and Re-fit a Model Call
validateFrequencyCutoffs
                        Validate frequency cutoffs
