Man pages for HIBAG
HIBAG -- HLA Genotype Imputation with Attribute Bagging
| HapMap_CEU_Geno | SNP genotypes of a study simulated from HapMap CEU genotypic... |
| HIBAG-package | HLA Genotype Imputation with Attribute Bagging |
| hlaAllele | A list of HLA types |
| hlaAlleleClass | Class of HLA Type |
| hlaAlleleDigit | Trim HLA alleles |
| hlaAlleleSubset | Get a subset of HLA types |
| hlaAttrBagClass | The class of HIBAG model |
| hlaAttrBagging | Build a HIBAG model |
| hlaAttrBagObj | The class of HIBAG object |
| hlaBED2Geno | Convert from PLINK BED format |
| hlaCheckSNPs | Check the SNP predictors in a HIBAG model |
| hlaClose | Dispose a model object |
| hlaCombineAllele | Combine two datasets of HLA types |
| hlaCombineModelObj | Combine two HIBAG models together |
| hlaCompareAllele | Evaluate prediction accuracies |
| hlaErrMsg | The last error message |
| hlaFlankingSNP | SNP IDs in Flanking Region |
| hlaGDS2Geno | Convert from SNP GDS format |
| hlaGeno2PED | Convert to PLINK PED format |
| hlaGenoAFreq | Allele Frequency |
| hlaGenoCombine | Combine two genotypic data sets into one |
| hlaGenoLD | Composite Linkage Disequilibrium |
| hlaGenoMFreq | Minor Allele Frequency |
| hlaGenoMRate | Missing Rates Per SNP |
| hlaGenoMRate_Samp | Missing Rates Per Sample |
| hlaGenoSubset | Get a subset of genotypes |
| hlaGenoSwitchStrand | Allele switching |
| hlaHaplo2Geno | Get a genotype object from a specified haplotype object |
| hlaHaploSubset | Get a subset of haplotypes |
| hlaLociInfo | HLA Locus Information |
| hlaMakeSNPGeno | Make a SNP genotype object |
| hlaMakeSNPHaplo | Make a SNP haplotype object |
| hlaModelFiles | Load a model object from files |
| hlaModelFromObj | Build a model from "hlaAttrBagObj" |
| hlaModelToObj | Convert "hlaAttrBagClass" to "hlaAttrBagObj" |
| hlaOutOfBag | Out-of-bag estimation of overall accuracy, per-allele... |
| hlaParallelAttrBagging | Build a HIBAG model via parallel computation |
| hlaPredMerge | Merge prediction results from multiple HIBAG models |
| hlaPublish | Finalize a HIBAG model |
| hlaReport | Format a report |
| hlaResource | Model Resource Information |
| hlaSampleAllele | Get sample IDs from HLA types with a filter |
| hlaSNPGenoClass | The class of SNP genotypes |
| hlaSNPHaploClass | The class of SNP haplotypes |
| hlaSNPID | Get SNP IDs and positions |
| hlaSplitAllele | Divide the samples randomly |
| hlaSubModelObj | Get a subset of individual classifiers |
| HLA_Type_Table | Four-digit HLA types of a study simulated from HapMap CEU |
| hlaUniqueAllele | Get unique HLA alleles |
| plot.hlaAttrBagClass | Plot a "hlaAttrBagClass" object |
| plot.hlaAttrBagObj | Plot a "hlaAttrBagObj" object |
| predict.hlaAttrBagClass | HIBAG model prediction (in parallel) |
| print.hlaAttrBagClass | Summarize a "hlaAttrBagClass" object |
| print.hlaAttrBagObj | Summarize a "hlaAttrBagObj" object |
| summary.hlaAlleleClass | Summarize a "hlaAlleleClass" object |
| summary.hlaAttrBagClass | Summarize a "hlaAttrBagClass" object |
| summary.hlaAttrBagObj | Summarize a "hlaAttrBagObj" object |
| summary.hlaSNPGenoClass | Summarize the genotypic dataset |
| summary.hlaSNPHaploClass | Summarize the haplotypic dataset |
