{ "_id": "6a1ac33f1d7bb097a09da2ab", "Package": "midasHLA", "Title": "R package for immunogenomics data handling and association\nanalysis", "Version": "1.21.0", "Authors@R": "c(\nperson(\"Christian\", \"Hammer\", email = \"hammerc6@gene.com\", role = \"aut\"),\nperson(\"Maciej\", \"Migdał\", email = \"mcjmigdal@gmail.com\", role = c(\"aut\", \"cre\")))", "Description": "MiDAS is a R package for immunogenetics data\ntransformation and statistical analysis. MiDAS accepts input\ndata in the form of HLA alleles and KIR types, and can\ntransform it into biologically meaningful variables, enabling\nHLA amino acid fine mapping, analyses of HLA evolutionary\ndivergence, KIR gene presence, as well as validated HLA-KIR\ninteractions. Further, it allows comprehensive statistical\nassociation analysis workflows with phenotypes of diverse\nmeasurement scales. MiDAS closes a gap between the inference of\nimmunogenetic variation and its efficient utilization to make\nrelevant discoveries related to T cell, Natural Killer cell,\nand disease biology.", "License": "MIT + file LICENCE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Collate": "'asserts.R' 'class.R' 'data.R' 'global.R' 'midasHLA.R'\n'parsingFunctions.R' 'stats.R' 'summarise.R'\n'transformationFunctions.R' 'utils.R'", "biocViews": "CellBiology, Genetics, StatisticalMethod", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:55:07 UTC", "RemoteUrl": "https://github.com/bioc/midasHLA", "RemoteRef": "HEAD", "RemoteSha": "3a3e981a2d4fdc6a34e70260d043b8dbd7913592", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:38:21 UTC", "User": "root" }, "Author": "Christian Hammer [aut],\nMaciej Migdał [aut, cre]", "Maintainer": "Maciej Migdał ", "MD5sum": "c7fc6a5e4149c799aa076033540cc782", "_user": "bioc", "_type": "src", "_file": "midasHLA_1.21.0.tar.gz", "_fileid": "28e73ba7f05f372dcbb9c23062cdc0e0473f897af147e53a06d5e83e1b1edee4", "_filesize": 2321476, "_sha256": "28e73ba7f05f372dcbb9c23062cdc0e0473f897af147e53a06d5e83e1b1edee4", "_created": "2026-05-30T07:38:21.000Z", "_published": "2026-05-30T11:00:15.630Z", "_jobs": [ { "job": 78634119534, "time": 196, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306561356" }, { "job": 78634119550, "time": 440, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306585126" }, { "job": 78634119575, "time": 438, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306584936" }, { "job": 78634119544, "time": 211, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7307679954" }, { "job": 78634119546, "time": 255, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7307682797" }, { "job": 78633793234, "time": 388, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306541302" }, { "job": 78634119536, "time": 177, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306559453" }, { "job": 78634119563, "time": 315, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306573216" }, { "job": 78634119570, "time": 396, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306581140" }, { "job": 78634119572, "time": 336, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306575237" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678169732", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/midasHLA", "_commit": { "id": "3a3e981a2d4fdc6a34e70260d043b8dbd7913592", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380907 }, "_maintainer": { "name": "Maciej Migdał", "email": "mcjmigdal@gmail.com", "login": "mcjmigdal", "linkedin": "in/mcjmigdal", "description": "Bioinformatician. 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"_exports": [ "analyzeAssociations", "analyzeConditionalAssociations", "checkAlleleFormat", "checkKirGenesFormat", "convertAlleleToVariable", "countsToVariables", "filterByFrequency", "filterByOmnibusGroups", "filterByVariables", "getAAFrequencies", "getAlleleResolution", "getAllelesForAA", "getExperiments", "getFrequencies", "getHlaCalls", "getHlaFrequencies", "getHlaKirInteractions", "getKirCalls", "getKIRFrequencies", "getOmnibusGroups", "getPlaceholder", "getVariableAAPos", "hlaCallsGranthamDistance", "hlaToAAVariation", "hlaToVariable", "HWETest", "kableResults", "omnibusTest", "prepareMiDAS", "readHlaAlignments", "readHlaCalls", "readKirCalls", "reduceAlleleResolution", "reduceHlaCalls", "runMiDAS", "summariseAAPosition" ], "_datasets": [ { "name": "allele_frequencies", "title": "Alleles frequencies scraped from allelefrequencies.net", "object": "allele_frequencies", "class": [ "data.frame" ], "fields": [ "var", "population", "frequency" ], "rows": 150640, "table": true, "tojson": true }, { "name": "dict_dist_grantham", "title": "Grantham distance", "object": "dict_dist_grantham", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "kir_frequencies", "title": "KIR genes frequencies scraped from allelefrequencies.net", "object": "kir_frequencies", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "var", "population", "frequency" ], "rows": 3744, "table": true, "tojson": true }, { "name": "MiDAS_tut_HLA", "title": "MiDAS tutorial HLA data", "object": "MiDAS_tut_HLA", "class": [ "data.frame" ], "fields": [ "ID", "A_1", "A_2", "B_1", "B_2", "C_1", "C_2", "DPA1_1", "DPA1_2", "DPB1_1", "DPB1_2", "DQA1_1", "DQA1_2", "DQB1_1", "DQB1_2", "DRA_1", "DRA_2", "DRB1_1", "DRB1_2" ], "rows": 1000, "table": true, "tojson": true }, { "name": "MiDAS_tut_KIR", "title": "MiDAS tutorial KIR data", "object": "MiDAS_tut_KIR", "class": [ "data.frame" ], "fields": [ "ID", "KIR3DL3", "KIR2DS2", "KIR2DL2", "KIR2DL3", "KIR2DP1", "KIR2DL1", "KIR3DP1", "KIR2DL4", "KIR3DL1", "KIR3DS1", "KIR2DL5", "KIR2DS3", "KIR2DS5", "KIR2DS4", "KIR2DS1", "KIR3DL2" ], "rows": 1000, "table": true, "tojson": true }, { "name": "MiDAS_tut_object", "title": "MiDAS tutorial MiDAS object", "object": "MiDAS_tut_object", "class": [ "MiDAS" ], "fields": [], "table": false, "tojson": false }, { "name": "MiDAS_tut_pheno", "title": "MiDAS tutorial phenotype data", "object": "MiDAS_tut_pheno", "class": [ "data.frame" ], "fields": [ "ID", "disease", "lab_value", "outcome" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "aaVariationToCounts", "title": "Transform amino acid variation data frame into counts table", "topics": [ "aaVariationToCounts" ] }, { "page": "adjustPValues", "title": "Adjust P-values for Multiple Comparisons", "topics": [ "adjustPValues" ] }, { "page": "allele_frequencies", "title": "Alleles frequencies scraped from allelefrequencies.net", "topics": [ "allele_frequencies" ] }, { "page": "analyzeAssociations", "title": "Association analysis", "topics": [ "analyzeAssociations" ] }, { "page": "analyzeConditionalAssociations", "title": "Stepwise conditional association analysis", "topics": [ "analyzeConditionalAssociations" ] }, { "page": "applyInheritanceModel", "title": "Apply inheritance model", "topics": [ "applyInheritanceModel", "applyInheritanceModel.matrix", "applyInheritanceModel.SummarizedExperiment" ] }, { "page": "as.data.frame.MiDAS", "title": "Coerce MiDAS to Data Frame", "topics": [ "as.data.frame.MiDAS" ] }, { "page": "backquote", "title": "Backquote character", "topics": [ "backquote" ] }, { "page": "characterMatches", "title": "Check if character matches one of possible values", "topics": [ "characterMatches" ] }, { "page": "checkAlleleFormat", "title": "Check HLA allele format", "topics": [ "checkAlleleFormat" ] }, { "page": "checkColDataFormat", "title": "Assert colData data", "topics": [ "checkColDataFormat" ] }, { "page": "checkHlaCallsFormat", "title": "Assert hla calls data frame format", "topics": [ "checkHlaCallsFormat" ] }, { "page": "checkKirCallsFormat", "title": "Assert KIR counts data frame format", "topics": [ "checkKirCallsFormat" ] }, { "page": "checkKirGenesFormat", "title": "Check KIR genes format", "topics": [ "checkKirGenesFormat" ] }, { "page": "checkStatisticalModel", "title": "Assert statistical model", "topics": [ "checkStatisticalModel" ] }, { "page": "colnamesMatches", "title": "Check column names", "topics": [ "colnamesMatches" ] }, { "page": "convertAlleleToVariable", "title": "Convert allele numbers to additional variables", "topics": [ "convertAlleleToVariable" ] }, { "page": "countsToVariables", "title": "Convert counts table to variables", "topics": [ "countsToVariables" ] }, { "page": "dfToExperimentMat", "title": "Helper transform data frame to experiment matrix", "topics": [ "dfToExperimentMat" ] }, { "page": "dict_dist_grantham", "title": "Grantham distance", "topics": [ "dict_dist_grantham" ] }, { "page": "distGrantham", "title": "Calculate Grantham distance between amino acid sequences", "topics": [ "distGrantham" ] }, { "page": "experimentMatToDf", "title": "Helper transform experiment matrix to data frame", "topics": [ "experimentMatToDf" ] }, { "page": "filterByFrequency", "title": "Filter MiDAS object by frequency", "topics": [ "filterByFrequency" ] }, { "page": "filterByOmnibusGroups", "title": "Filter MiDAS object by omnibus groups", "topics": [ "filterByOmnibusGroups" ] }, { "page": "filterByVariables", "title": "Filter MiDAS object by features", "topics": [ "filterByVariables" ] }, { "page": "filterExperimentByFrequency", "title": "Filter experiment by frequency", "topics": [ "filterExperimentByFrequency", "filterExperimentByFrequency.matrix", "filterExperimentByFrequency.SummarizedExperiment" ] }, { "page": "filterExperimentByVariables", "title": "Filter experiment by variable", "topics": [ "filterExperimentByVariables", "filterExperimentByVariables.matrix", "filterExperimentByVariables.SummarizedExperiment" ] }, { "page": "filterListByElements", "title": "Filter list by elements", "topics": [ "filterListByElements" ] }, { "page": "formatResults", "title": "Pretty format statistical analysis results helper", "topics": [ "formatResults" ] }, { "page": "getAAFrequencies", "title": "Calculate amino acid frequencies", "topics": [ "getAAFrequencies" ] }, { "page": "getAlleleResolution", "title": "Infer HLA allele resolution", "topics": [ "getAlleleResolution" ] }, { "page": "getAllelesForAA", "title": "Get HLA alleles for amino acid position", "topics": [ "getAllelesForAA" ] }, { "page": "getExperimentFrequencies", "title": "Calculate experiment's features frequencies", "topics": [ "getExperimentFrequencies", "getExperimentFrequencies.matrix", "getExperimentFrequencies.SummarizedExperiment" ] }, { "page": "getExperimentPopulationMultiplicator", "title": "Get experiment's population multiplicator", "topics": [ "getExperimentPopulationMultiplicator", "getExperimentPopulationMultiplicator.matrix", "getExperimentPopulationMultiplicator.SummarizedExperiment" ] }, { "page": "getExperiments", "title": "Get available experiments in MiDAS object.", "topics": [ "getExperiments" ] }, { "page": "getFrequencies", "title": "Calculate features frequencies for a given experiment in MiDAS object.", "topics": [ "getFrequencies" ] }, { "page": "getFrequencyMask", "title": "Helper function for filtering frequency data frame", "topics": [ "getFrequencyMask" ] }, { "page": "getHlaCalls", "title": "Get HLA calls from MiDAS object.", "topics": [ "getHlaCalls" ] }, { "page": "getHlaCallsGenes", "title": "Get HLA calls genes", "topics": [ "getHlaCallsGenes" ] }, { "page": "getHlaFrequencies", "title": "Calculate HLA allele frequencies", "topics": [ "getHlaFrequencies" ] }, { "page": "getHlaKirInteractions", "title": "Get HLA - KIR interactions", "topics": [ "getHlaKirInteractions" ] }, { "page": "getKirCalls", "title": "Get KIR calls from MiDAS object.", "topics": [ "getKirCalls" ] }, { "page": "getKIRFrequencies", "title": "Calculate KIR genes frequencies", "topics": [ "getKIRFrequencies" ] }, { "page": "getObjectDetails", "title": "Get attributes of statistical model object", "topics": [ "getObjectDetails" ] }, { "page": "getOmnibusGroups", "title": "Get omnibus groups from MiDAS object.", "topics": [ "getOmnibusGroups" ] }, { "page": "getPlaceholder", "title": "Get placeholder name from MiDAS object.", "topics": [ "getPlaceholder" ] }, { "page": "getReferenceFrequencies", "title": "Helper transforming reference frequencies", "topics": [ "getReferenceFrequencies" ] }, { "page": "getVariableAAPos", "title": "Find variable positions in sequence alignment", "topics": [ "getVariableAAPos" ] }, { "page": "hasTidyMethod", "title": "Check if tidy method for class exist", "topics": [ "hasTidyMethod" ] }, { "page": "hlaAlignmentGrantham", "title": "Helper function returning alignment for Grantham distance calculations", "topics": [ "hlaAlignmentGrantham" ] }, { "page": "hlaCallsGranthamDistance", "title": "Calculate Grantham distance between HLA alleles", "topics": [ "hlaCallsGranthamDistance" ] }, { "page": "hlaCallsToCounts", "title": "Transform HLA calls to counts table", "topics": [ "hlaCallsToCounts" ] }, { "page": "hlaToAAVariation", "title": "Generate amino acid variation matrix", "topics": [ "hlaToAAVariation" ] }, { "page": "hlaToVariable", "title": "Convert HLA calls to variables", "topics": [ "hlaToVariable" ] }, { "page": "HWETest", "title": "Test for Hardy Weinberg equilibrium", "topics": [ "HWETest" ] }, { "page": "isCharacterOrNULL", "title": "Check if object is character vector or NULL", "topics": [ "isCharacterOrNULL" ] }, { "page": "isClass", "title": "Check if object is of class x", "topics": [ "isClass" ] }, { "page": "isClassOrNULL", "title": "Check if object is of class x or null", "topics": [ "isClassOrNULL" ] }, { "page": "isCountOrNULL", "title": "Check if object is count or NULL", "topics": [ "isCountOrNULL" ] }, { "page": "isCountsOrZeros", "title": "Check if vector contains only counts or zeros", "topics": [ "isCountsOrZeros" ] }, { "page": "isExperimentCountsOrZeros", "title": "Check if frequencies can be calculated for an experiment", "topics": [ "isExperimentCountsOrZeros" ] }, { "page": "isExperimentInheritanceModelApplicable", "title": "Check if experiment is inheritance model applicable", "topics": [ "isExperimentInheritanceModelApplicable", "isExperimentInheritanceModelApplicable.matrix", "isExperimentInheritanceModelApplicable.SummarizedExperiment" ] }, { "page": "isFlagOrNULL", "title": "Check if object is flag or NULL", "topics": [ "isFlagOrNULL" ] }, { "page": "isNumberOrNULL", "title": "Check if object is number or NULL", "topics": [ "isNumberOrNULL" ] }, { "page": "isStringOrNULL", "title": "Check if object is string or NULL", "topics": [ "isStringOrNULL" ] }, { "page": "isTRUEorFALSE", "title": "Check if object is TRUE or FALSE flag", "topics": [ "isTRUEorFALSE" ] }, { "page": "iterativeLRT", "title": "Iterative likelihood ratio test", "topics": [ "iterativeLRT" ] }, { "page": "iterativeModel", "title": "Iteratively evaluate model for different variables", "topics": [ "iterativeModel" ] }, { "page": "kableResults", "title": "Create association analysis results table in HTML or LaTeX", "topics": [ "kableResults" ] }, { "page": "kir_frequencies", "title": "KIR genes frequencies scraped from allelefrequencies.net", "topics": [ "kir_frequencies" ] }, { "page": "lapply_tryCatch", "title": "lapply with tryCatch routine", "topics": [ "lapply_tryCatch" ] }, { "page": "listMiDASDictionaries", "title": "List HLA alleles dictionaries", "topics": [ "listMiDASDictionaries" ] }, { "page": "LRTest", "title": "Likelihood ratio test", "topics": [ "LRTest" ] }, { "page": "MiDAS_tut_HLA", "title": "MiDAS tutorial HLA data", "topics": [ "MiDAS_tut_HLA" ] }, { "page": "MiDAS_tut_KIR", "title": "MiDAS tutorial KIR data", "topics": [ "MiDAS_tut_KIR" ] }, { "page": "MiDAS_tut_object", "title": "MiDAS tutorial MiDAS object", "topics": [ "MiDAS_tut_object" ] }, { "page": "MiDAS_tut_pheno", "title": "MiDAS tutorial phenotype data", "topics": [ "MiDAS_tut_pheno" ] }, { "page": "MiDAS-class", "title": "MiDAS class", "topics": [ "filterByFrequency,MiDAS-method", "filterByOmnibusGroups,MiDAS-method", "filterByVariables,MiDAS-method", "getAllelesForAA,MiDAS-method", "getExperiments,MiDAS-method", "getFrequencies,MiDAS-method", "getHlaCalls,MiDAS-method", "getKirCalls,MiDAS-method", "getOmnibusGroups,MiDAS-method", "getPlaceholder,MiDAS-method", "MiDAS", "MiDAS-class" ] }, { "page": "midasToWide", "title": "Transform MiDAS to wide format data.frame", "topics": [ "midasToWide" ] }, { "page": "objectHasPlaceholder", "title": "Check if placeholder is present in object formula", "topics": [ "objectHasPlaceholder" ] }, { "page": "omnibusTest", "title": "Omnibus test", "topics": [ "omnibusTest" ] }, { "page": "prepareMiDAS", "title": "Construct a MiDAS object", "topics": [ "prepareMiDAS" ] }, { "page": "prepareMiDAS_hla_aa", "title": "Prepare MiDAS data on HLA amino acid level", "topics": [ "prepareMiDAS_hla_aa" ] }, { "page": "prepareMiDAS_hla_alleles", "title": "Prepare MiDAS data on HLA allele level", "topics": [ "prepareMiDAS_hla_alleles" ] }, { "page": "prepareMiDAS_hla_custom", "title": "Prepare MiDAS data on custom HLA level", "topics": [ "prepareMiDAS_hla_custom" ] }, { "page": "prepareMiDAS_hla_divergence", "title": "Prepare MiDAS data on HLA divergence level", "topics": [ "prepareMiDAS_hla_divergence" ] }, { "page": "prepareMiDAS_hla_g_groups", "title": "Prepare MiDAS data on HLA allele's G groups level", "topics": [ "prepareMiDAS_hla_g_groups" ] }, { "page": "prepareMiDAS_hla_het", "title": "Prepare MiDAS data on HLA heterozygosity level", "topics": [ "prepareMiDAS_hla_het" ] }, { "page": "prepareMiDAS_hla_kir_interactions", "title": "Prepare MiDAS data on HLA - KIR interactions level", "topics": [ "prepareMiDAS_hla_kir_interactions" ] }, { "page": "prepareMiDAS_hla_NK_ligands", "title": "Prepare MiDAS data on HLA allele's groups level", "topics": [ "prepareMiDAS_hla_NK_ligands" ] }, { "page": "prepareMiDAS_hla_supertypes", "title": "Prepare MiDAS data on HLA allele's supertypes level", "topics": [ "prepareMiDAS_hla_supertypes" ] }, { "page": "prepareMiDAS_kir_custom", "title": "Prepare MiDAS data on custom KIR level", "topics": [ "prepareMiDAS_kir_custom" ] }, { "page": "prepareMiDAS_kir_genes", "title": "Prepare MiDAS data on KIR genes level", "topics": [ "prepareMiDAS_kir_genes" ] }, { "page": "prepareMiDAS_kir_haplotypes", "title": "Prepare MiDAS data on KIR haplotypes level", "topics": [ "prepareMiDAS_kir_haplotypes" ] }, { "page": "readHlaAlignments", "title": "Read HLA allele alignments", "topics": [ "readHlaAlignments" ] }, { "page": "readHlaCalls", "title": "Read HLA allele calls", "topics": [ "readHlaCalls" ] }, { "page": "readKirCalls", "title": 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