# R package for immunogenomics data handling and association analysis

## Documentation for package ‘midasHLA’ version 1.19.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I K L M O P R S U V

## -- A --

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
applyInheritanceModel.matrix | Apply inheritance model
applyInheritanceModel.SummarizedExperiment | Apply inheritance model
as.data.frame.MiDAS | Coerce MiDAS to Data Frame

## -- B --

backquote | Backquote character

## -- C --

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

## -- D --

dfToExperimentMat | Helper transform data frame to experiment matrix
dict_dist_grantham | Grantham distance
distGrantham | Calculate Grantham distance between amino acid sequences

## -- E --

experimentMatToDf | Helper transform experiment matrix to data frame

## -- F --

filterByFrequency | Filter MiDAS object by frequency
filterByFrequency-method | MiDAS class
filterByOmnibusGroups | Filter MiDAS object by omnibus groups
filterByOmnibusGroups-method | MiDAS class
filterByVariables | Filter MiDAS object by features
filterByVariables-method | MiDAS class
filterExperimentByFrequency | Filter experiment by frequency
filterExperimentByFrequency.matrix | Filter experiment by frequency
filterExperimentByFrequency.SummarizedExperiment | Filter experiment by frequency
filterExperimentByVariables | Filter experiment by variable
filterExperimentByVariables.matrix | Filter experiment by variable
filterExperimentByVariables.SummarizedExperiment | Filter experiment by variable
filterListByElements | Filter list by elements
formatResults | Pretty format statistical analysis results helper

## -- G --

getAAFrequencies | Calculate amino acid frequencies
getAlleleResolution | Infer HLA allele resolution
getAllelesForAA | Get HLA alleles for amino acid position
getAllelesForAA-method | MiDAS class
getExperimentFrequencies | Calculate experiment's features frequencies
getExperimentFrequencies.matrix | Calculate experiment's features frequencies
getExperimentFrequencies.SummarizedExperiment | Calculate experiment's features frequencies
getExperimentPopulationMultiplicator | Get experiment's population multiplicator
getExperimentPopulationMultiplicator.matrix | Get experiment's population multiplicator
getExperimentPopulationMultiplicator.SummarizedExperiment | Get experiment's population multiplicator
getExperiments | Get available experiments in MiDAS object.
getExperiments-method | MiDAS class
getFrequencies | Calculate features frequencies for a given experiment in MiDAS object.
getFrequencies-method | MiDAS class
getFrequencyMask | Helper function for filtering frequency data frame
getHlaCalls | Get HLA calls from MiDAS object.
getHlaCalls-method | MiDAS class
getHlaCallsGenes | Get HLA calls genes
getHlaFrequencies | Calculate HLA allele frequencies
getHlaKirInteractions | Get HLA - KIR interactions
getKirCalls | Get KIR calls from MiDAS object.
getKirCalls-method | MiDAS class
getKIRFrequencies | Calculate KIR genes frequencies
getObjectDetails | Get attributes of statistical model object
getOmnibusGroups | Get omnibus groups from MiDAS object.
getOmnibusGroups-method | MiDAS class
getPlaceholder | Get placeholder name from MiDAS object.
getPlaceholder-method | MiDAS class
getReferenceFrequencies | Helper transforming reference frequencies
getVariableAAPos | Find variable positions in sequence alignment

## -- H --

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
HWETest | Test for Hardy Weinberg equilibrium

## -- I --

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
isExperimentInheritanceModelApplicable.matrix | Check if experiment is inheritance model applicable
isExperimentInheritanceModelApplicable.SummarizedExperiment | 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

## -- K --

kableResults | Create association analysis results table in HTML or LaTeX
kir_frequencies | KIR genes frequencies scraped from allelefrequencies.net

## -- L --

lapply_tryCatch | lapply with tryCatch routine
listMiDASDictionaries | List HLA alleles dictionaries
LRTest | Likelihood ratio test

## -- M --

MiDAS | MiDAS class
MiDAS-class | MiDAS class
midasToWide | Transform MiDAS to wide format data.frame
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

## -- O --

objectHasPlaceholder | Check if placeholder is present in object formula
omnibusTest | Omnibus test

## -- P --

prepareMiDAS | Construct a MiDAS object
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_NK_ligands | Prepare MiDAS data on HLA allele's groups 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

## -- R --

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

## -- S --

stringMatches | Check if string matches one of possible values
summariseAAPosition | Summarize amino acid position

## -- U --

updateModel | Extend and Re-fit a Model Call

## -- V --

validateFrequencyCutoffs | Validate frequency cutoffs