API for Genentech/midasHLA
R package for immunogenomics data handling and association analysis
| Global functions | |
|---|---|
| HWETest | Man page Source code |
| LRTest | Man page Source code |
| MiDAS | Man page |
| MiDAS-class | Man page |
| MiDAS_tut_HLA | Man page |
| MiDAS_tut_KIR | Man page |
| MiDAS_tut_object | Man page |
| MiDAS_tut_pheno | Man page |
| aaVariationToCounts | Man page Source code |
| adjustPValues | Man page Source code |
| allele_frequencies | Man page |
| analyzeAssociations | Man page Source code |
| analyzeConditionalAssociations | Man page Source code |
| applyInheritanceModel | Man page Source code |
| applyInheritanceModel.SummarizedExperiment | Man page Source code |
| applyInheritanceModel.matrix | Man page Source code |
| as.data.frame.MiDAS | Man page Source code |
| backquote | Man page Source code |
| characterMatches | Man page Source code |
| checkAlleleFormat | Man page Source code |
| checkColDataFormat | Man page Source code |
| checkHlaCallsFormat | Man page Source code |
| checkKirCallsFormat | Man page Source code |
| checkKirGenesFormat | Man page Source code |
| checkStatisticalModel | Man page Source code |
| colnamesMatches | Man page Source code |
| convertAlleleToVariable | Man page Source code |
| countsToVariables | Man page Source code |
| dfToExperimentMat | Man page Source code |
| dict_dist_grantham | Man page |
| distGrantham | Man page Source code |
| experimentMatToDf | Man page Source code |
| filterByFrequency | Man page |
| filterByFrequency,MiDAS-method | Man page |
| filterByOmnibusGroups | Man page |
| filterByOmnibusGroups,MiDAS-method | Man page |
| filterByVariables | Man page |
| filterByVariables,MiDAS-method | Man page |
| filterExperimentByFrequency | Man page Source code |
| filterExperimentByFrequency.SummarizedExperiment | Man page Source code |
| filterExperimentByFrequency.matrix | Man page Source code |
| filterExperimentByVariables | Man page Source code |
| filterExperimentByVariables.SummarizedExperiment | Man page Source code |
| filterExperimentByVariables.matrix | Man page Source code |
| filterListByElements | Man page Source code |
| formatResults | Man page Source code |
| getAAFrequencies | Man page Source code |
| getAlleleResolution | Man page Source code |
| getAllelesForAA | Man page |
| getAllelesForAA,MiDAS-method | Man page |
| getExperimentFrequencies | Man page Source code |
| getExperimentFrequencies.SummarizedExperiment | Man page Source code |
| getExperimentFrequencies.matrix | Man page Source code |
| getExperimentPopulationMultiplicator | Man page Source code |
| getExperimentPopulationMultiplicator.SummarizedExperiment | Man page Source code |
| getExperimentPopulationMultiplicator.matrix | Man page Source code |
| getExperiments | Man page |
| getExperiments,MiDAS-method | Man page |
| getFrequencies | Man page |
| getFrequencies,MiDAS-method | Man page |
| getFrequencyMask | Man page Source code |
| getHlaCalls | Man page |
| getHlaCalls,MiDAS-method | Man page |
| getHlaCallsGenes | Man page Source code |
| getHlaFrequencies | Man page Source code |
| getHlaKirInteractions | Man page Source code |
| getKIRFrequencies | Man page Source code |
| getKirCalls | Man page |
| getKirCalls,MiDAS-method | Man page |
| getObjectDetails | Man page Source code |
| getOmnibusGroups | Man page |
| getOmnibusGroups,MiDAS-method | Man page |
| getPlaceholder | Man page |
| getPlaceholder,MiDAS-method | Man page |
| getReferenceFrequencies | Man page Source code |
| getVariableAAPos | Man page Source code |
| hasTidyMethod | Man page Source code |
| hlaAlignmentGrantham | Man page Source code |
| hlaCallsGranthamDistance | Man page Source code |
| hlaCallsToCounts | Man page Source code |
| hlaToAAVariation | Man page Source code |
| hlaToVariable | Man page Source code |
| isCharacterOrNULL | Man page Source code |
| isClass | Man page Source code |
| isClassOrNULL | Man page Source code |
| isCountOrNULL | Man page Source code |
| isCountsOrZeros | Man page Source code |
| isExperimentCountsOrZeros | Man page Source code |
| isExperimentInheritanceModelApplicable | Man page Source code |
| isExperimentInheritanceModelApplicable.SummarizedExperiment | Man page Source code |
| isExperimentInheritanceModelApplicable.matrix | Man page Source code |
| isFlagOrNULL | Man page Source code |
| isNumberOrNULL | Man page Source code |
| isStringOrNULL | Man page Source code |
| isTRUEorFALSE | Man page Source code |
| iterativeLRT | Man page Source code |
| iterativeModel | Man page Source code |
| kableResults | Man page Source code |
| kir_frequencies | Man page |
| lapply_tryCatch | Man page Source code |
| listMiDASDictionaries | Man page Source code |
| midasToWide | Man page Source code |
| objectHasPlaceholder | Man page Source code |
| omnibusTest | Man page Source code |
| prepareMiDAS | Man page Source code |
| prepareMiDAS_hla_NK_ligands | Man page Source code |
| prepareMiDAS_hla_aa | Man page Source code |
| prepareMiDAS_hla_alleles | Man page Source code |
| prepareMiDAS_hla_custom | Man page Source code |
| prepareMiDAS_hla_divergence | Man page Source code |
| prepareMiDAS_hla_g_groups | Man page Source code |
| prepareMiDAS_hla_het | Man page Source code |
| prepareMiDAS_hla_kir_interactions | Man page Source code |
| prepareMiDAS_hla_supertypes | Man page Source code |
| prepareMiDAS_kir_custom | Man page Source code |
| prepareMiDAS_kir_genes | Man page Source code |
| prepareMiDAS_kir_haplotypes | Man page Source code |
| readHlaAlignments | Man page Source code |
| readHlaCalls | Man page Source code |
| readKirCalls | Man page Source code |
| reduceAlleleResolution | Man page Source code |
| reduceHlaCalls | Man page Source code |
| runMiDAS | Man page Source code |
| runMiDASGetVarsFreq | Man page Source code |
| runMiDAS_conditional | Source code |
| runMiDAS_conditional_omnibus | Source code |
| runMiDAS_linear | Source code |
| runMiDAS_linear_omnibus | Source code |
| stringMatches | Man page Source code |
| summariseAAPosition | Man page Source code |
| updateModel | Man page Source code |
| validateFrequencyCutoffs | Man page Source code |
