├── .Rbuildignore ├── .gitattributes ├── .github └── workflows │ └── r.yml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── Association.R ├── DataUtilities.R ├── HIBAG.R └── SeqFormat.R ├── README.md ├── data ├── HLA_Type_Table.rdata └── HapMap_CEU_Geno.rdata ├── inst ├── CITATION ├── GPLv3 ├── doc │ ├── GeneInfo_hg18.txt │ ├── GeneInfo_hg19.txt │ ├── GeneInfo_hg38.txt │ ├── HIBAG_LICENSE.txt │ └── case_control.txt ├── extdata │ ├── HapMap_CEU.bed │ ├── HapMap_CEU.bim │ ├── HapMap_CEU.fam │ ├── HapMap_CEU_Chr6.gds │ ├── ModelList.RData │ ├── OutOfBag.RData │ ├── case_control.txt.xz │ └── v3.22.0 │ │ ├── FeatureInfo.txt │ │ ├── Licence.txt │ │ ├── SeqAlign │ │ ├── a_prot.txt.xz │ │ ├── b_prot.txt.xz │ │ ├── c_prot.txt.xz │ │ ├── dpa1_prot.txt.xz │ │ ├── dpb1_prot.txt.xz │ │ ├── dqa1_prot.txt.xz │ │ ├── dqb1_prot.txt.xz │ │ └── drb1_prot.txt.xz │ │ ├── hla_nom_g.txt.xz │ │ └── hla_nom_p.txt.xz └── include │ └── LibHLA_ext.h ├── man ├── HIBAG-package.Rd ├── HLA_Type_Table.Rd ├── HapMap_CEU_Geno.Rd ├── hlaAASeqClass.Rd ├── hlaAllele.Rd ├── hlaAlleleClass.Rd ├── hlaAlleleDigit.Rd ├── hlaAlleleSubset.Rd ├── hlaAlleleToVCF.Rd ├── hlaAssocTest.Rd ├── hlaAttrBagClass.Rd ├── hlaAttrBagObj.Rd ├── hlaAttrBagging.Rd ├── hlaBED2Geno.Rd ├── hlaCheckAllele.Rd ├── hlaCheckSNPs.Rd ├── hlaClose.Rd ├── hlaCombineAllele.Rd ├── hlaCombineModelObj.Rd ├── hlaCompareAllele.Rd ├── hlaConvSequence.Rd ├── hlaDistance.Rd ├── hlaFlankingSNP.Rd ├── hlaGDS2Geno.Rd ├── hlaGeno2PED.Rd ├── hlaGenoAFreq.Rd ├── hlaGenoCombine.Rd ├── hlaGenoLD.Rd ├── hlaGenoMFreq.Rd ├── hlaGenoMRate.Rd ├── hlaGenoMRate_Samp.Rd ├── hlaGenoSubset.Rd ├── hlaGenoSwitchStrand.Rd ├── hlaLDMatrix.Rd ├── hlaLociInfo.Rd ├── hlaMakeSNPGeno.Rd ├── hlaModelFiles.Rd ├── hlaModelFromObj.Rd ├── hlaOutOfBag.Rd ├── hlaParallelAttrBagging.Rd ├── hlaPredMerge.Rd ├── hlaPredict.Rd ├── hlaPublish.Rd ├── hlaReport.Rd ├── hlaReportPlot.Rd ├── hlaSNPGenoClass.Rd ├── hlaSNPID.Rd ├── hlaSampleAllele.Rd ├── 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