Man pages for Genentech/midasHLA
R package for immunogenomics data handling and association analysis
| 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 |
| as.data.frame.MiDAS | Coerce MiDAS to Data Frame |
| backquote | Backquote character |
| 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 |
| dfToExperimentMat | Helper transform data frame to experiment matrix |
| dict_dist_grantham | Grantham distance |
| distGrantham | Calculate Grantham distance between amino acid sequences |
| experimentMatToDf | Helper transform experiment matrix to data frame |
| filterByFrequency | Filter MiDAS object by frequency |
| filterByOmnibusGroups | Filter MiDAS object by omnibus groups |
| filterByVariables | Filter MiDAS object by features |
| filterExperimentByFrequency | Filter experiment by frequency |
| filterExperimentByVariables | Filter experiment by variable |
| filterListByElements | Filter list by elements |
| formatResults | Pretty format statistical analysis results helper |
| getAAFrequencies | Calculate amino acid frequencies |
| getAlleleResolution | Infer HLA allele resolution |
| getAllelesForAA | Get HLA alleles for amino acid position |
| getExperimentFrequencies | Calculate experiment's features frequencies |
| getExperimentPopulationMultiplicator | Get experiment's population multiplicator |
| getExperiments | Get available experiments in MiDAS object. |
| getFrequencies | Calculate features frequencies for a given experiment in... |
| getFrequencyMask | Helper function for filtering frequency data frame |
| getHlaCalls | Get HLA calls from MiDAS object. |
| getHlaCallsGenes | Get HLA calls genes |
| getHlaFrequencies | Calculate HLA allele frequencies |
| getHlaKirInteractions | Get HLA - KIR interactions |
| getKirCalls | Get KIR calls from MiDAS object. |
| getKIRFrequencies | Calculate KIR genes frequencies |
| getObjectDetails | Get attributes of statistical model object |
| getOmnibusGroups | Get omnibus groups from MiDAS object. |
| getPlaceholder | Get placeholder name from MiDAS object. |
| getReferenceFrequencies | Helper transforming reference frequencies |
| getVariableAAPos | Find variable positions in sequence alignment |
| hasTidyMethod | Check if tidy method for class exist |
| hlaAlignmentGrantham | Helper function returning alignment for Grantham distance... |
| 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 |
| 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 |
| 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 |
| kableResults | Create association analysis results table in HTML or LaTeX |
| kir_frequencies | KIR genes frequencies scraped from allelefrequencies.net |
| lapply_tryCatch | lapply with tryCatch routine |
| listMiDASDictionaries | List HLA alleles dictionaries |
| LRTest | Likelihood ratio test |
| 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 |
| objectHasPlaceholder | Check if placeholder is present in object formula |
| omnibusTest | Omnibus test |
| 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 |
| 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 |
| stringMatches | Check if string matches one of possible values |
| summariseAAPosition | Summarize amino acid position |
| updateModel | Extend and Re-fit a Model Call |
| validateFrequencyCutoffs | Validate frequency cutoffs |
