Files in Genentech/midasHLA

R package for immunogenomics data handling and association analysis

NEWS.md R/asserts.R R/class.R R/data.R R/global.R R/midasHLA.R R/parsingFunctions.R R/stats.R R/summarise.R R/transformationFunctions.R R/utils.R README.md data-raw/MiDAS_tut_HLA.R data-raw/MiDAS_tut_KIR.R data-raw/MiDAS_tut_object.R data-raw/MiDAS_tut_pheno.R data-raw/allele_frequencies.R data-raw/dict_dist_grantham.R data-raw/kir_frequencies.R inst/benchmark/prepareMiDAS_hla_aa.R inst/benchmark/prepareMiDAS_hla_alleles.R inst/benchmark/simulateHlaCalls.R inst/benchmark/workflow_hla_aa.R inst/benchmark/workflow_hla_alleles.R inst/scripts/download_extdata.R inst/scripts/parse_alignments.R longtests/testthat.R longtests/testthat/test_class.R longtests/testthat/test_stats.R man/HWETest.Rd man/LRTest.Rd man/MiDAS-class.Rd man/MiDAS_tut_HLA.Rd man/MiDAS_tut_KIR.Rd man/MiDAS_tut_object.Rd man/MiDAS_tut_pheno.Rd man/aaVariationToCounts.Rd man/adjustPValues.Rd man/allele_frequencies.Rd man/analyzeAssociations.Rd man/analyzeConditionalAssociations.Rd man/applyInheritanceModel.Rd man/as.data.frame.MiDAS.Rd man/backquote.Rd man/characterMatches.Rd man/checkAlleleFormat.Rd man/checkColDataFormat.Rd man/checkHlaCallsFormat.Rd man/checkKirCallsFormat.Rd man/checkKirGenesFormat.Rd man/checkStatisticalModel.Rd man/colnamesMatches.Rd man/convertAlleleToVariable.Rd man/countsToVariables.Rd man/dfToExperimentMat.Rd man/dict_dist_grantham.Rd man/distGrantham.Rd man/experimentMatToDf.Rd man/filterByFrequency.Rd man/filterByOmnibusGroups.Rd man/filterByVariables.Rd man/filterExperimentByFrequency.Rd man/filterExperimentByVariables.Rd man/filterListByElements.Rd man/formatResults.Rd man/getAAFrequencies.Rd man/getAlleleResolution.Rd man/getAllelesForAA.Rd man/getExperimentFrequencies.Rd man/getExperimentPopulationMultiplicator.Rd man/getExperiments.Rd man/getFrequencies.Rd man/getFrequencyMask.Rd man/getHlaCalls.Rd man/getHlaCallsGenes.Rd man/getHlaFrequencies.Rd man/getHlaKirInteractions.Rd man/getKIRFrequencies.Rd man/getKirCalls.Rd man/getObjectDetails.Rd man/getOmnibusGroups.Rd man/getPlaceholder.Rd man/getReferenceFrequencies.Rd man/getVariableAAPos.Rd man/hasTidyMethod.Rd man/hlaAlignmentGrantham.Rd man/hlaCallsGranthamDistance.Rd man/hlaCallsToCounts.Rd man/hlaToAAVariation.Rd man/hlaToVariable.Rd man/isCharacterOrNULL.Rd man/isClass.Rd man/isClassOrNULL.Rd man/isCountOrNULL.Rd man/isCountsOrZeros.Rd man/isExperimentCountsOrZeros.Rd man/isExperimentInheritanceModelApplicable.Rd man/isFlagOrNULL.Rd man/isNumberOrNULL.Rd man/isStringOrNULL.Rd man/isTRUEorFALSE.Rd man/iterativeLRT.Rd man/iterativeModel.Rd man/kableResults.Rd man/kir_frequencies.Rd man/lapply_tryCatch.Rd man/listMiDASDictionaries.Rd man/midasToWide.Rd man/objectHasPlaceholder.Rd man/omnibusTest.Rd man/prepareMiDAS.Rd man/prepareMiDAS_hla_NK_ligands.Rd man/prepareMiDAS_hla_aa.Rd man/prepareMiDAS_hla_alleles.Rd man/prepareMiDAS_hla_custom.Rd man/prepareMiDAS_hla_divergence.Rd man/prepareMiDAS_hla_g_groups.Rd man/prepareMiDAS_hla_het.Rd man/prepareMiDAS_hla_kir_interactions.Rd man/prepareMiDAS_hla_supertypes.Rd man/prepareMiDAS_kir_custom.Rd man/prepareMiDAS_kir_genes.Rd man/prepareMiDAS_kir_haplotypes.Rd man/readHlaAlignments.Rd man/readHlaCalls.Rd man/readKirCalls.Rd man/reduceAlleleResolution.Rd man/reduceHlaCalls.Rd man/runMiDAS.Rd man/runMiDASGetVarsFreq.Rd man/stringMatches.Rd man/summariseAAPosition.Rd man/updateModel.Rd man/validateFrequencyCutoffs.Rd tests/testthat.R tests/testthat/test_asserts.R tests/testthat/test_class.R tests/testthat/test_parsing.R tests/testthat/test_stats.R tests/testthat/test_summarise.R tests/testthat/test_transformation.R tests/testthat/test_utils.R vignettes/MiDAS_tutorial.Rmd vignettes/MiDAS_vignette.Rmd