R package for immunogenomics data handling and association analysis


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Documentation for package ‘midasHLA’ version 1.4.0

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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