R package for immunogenomics data handling and association analysis

Documentation for package ‘midasHLA’ version 1.6.0

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-- 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