Function reference • midasHLA

All functions
`HWETest()`	Test for Hardy Weinberg equilibrium
`LRTest()`	Likelihood ratio test
`getExperiments(<MiDAS>)` `getHlaCalls(<MiDAS>)` `getKirCalls(<MiDAS>)` `getPlaceholder(<MiDAS>)` `getOmnibusGroups(<MiDAS>)` `getFrequencies(<MiDAS>)` `filterByFrequency(<MiDAS>)` `filterByOmnibusGroups(<MiDAS>)` `filterByVariables(<MiDAS>)` `getAllelesForAA(<MiDAS>)`	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

Reference

All functions