Man pages for zhengxwen/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 |
| hlaAASeqClass | Class of HLA Amino Acid Sequence Type |
| hlaAllele | A list of HLA/KIR types |
| hlaAlleleClass | Class of HLA/KIR Type |
| hlaAlleleDigit | Trim HLA alleles |
| hlaAlleleSubset | Get a subset of HLA/KIR types |
| hlaAlleleToVCF | Convert HLA alleles to VCF |
| hlaAssocTest | Statistical Association Tests |
| hlaAttrBagClass | The class of HIBAG model |
| hlaAttrBagging | Build a HIBAG model |
| hlaAttrBagObj | The class of HIBAG object |
| hlaBED2Geno | Convert from PLINK BED format |
| hlaCheckAllele | Check SNP alleles |
| 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 |
| hlaConvSequence | Conversion From HLA Alleles to Amino Acid Sequences |
| hlaDistance | Distance matrix of HLA alleles |
| hlaFlankingSNP | SNP IDs or SNP genotypes in Flanking Region |
| hlaGDS2Geno | Import genotypes from a GDS file |
| 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 flipping if needed |
| hlaLDMatrix | Composite Linkage Disequilibrium in a Region |
| hlaLociInfo | HLA/KIR Locus Information |
| hlaMakeSNPGeno | Make a SNP genotype object |
| hlaModelFiles | Load a model object from files |
| hlaModelFromObj | Conversion between the in-memory model and the object that... |
| hlaOutOfBag | Out-of-bag estimation of overall accuracy, per-allele... |
| hlaParallelAttrBagging | Build a HIBAG model via parallel computation |
| hlaPredict | HIBAG model prediction (in parallel) |
| hlaPredMerge | Merge prediction results from multiple HIBAG models |
| hlaPublish | Finalize a HIBAG model |
| hlaReport | Format a report |
| hlaReportPlot | Format a report with figures |
| hlaSampleAllele | Get sample IDs from HLA types with a filter |
| hlaSetKernelTarget | Set the CPU target |
| hlaSNPGenoClass | The class of SNP genotypes |
| 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.hlaAttrBagObj | Plot a HIBAG model |
| print.hlaAttrBagClass | Summarize a "hlaAttrBagClass" or "hlaAttrBagObj" object. |
| summary.hlaAlleleClass | Summarize a "hlaAlleleClass" or "hlaAASeqClass" object |
| summary.hlaSNPGenoClass | Summarize a SNP dataset |
