HIBAG: HLA Genotype Imputation with Attribute Bagging

It is a software package for imputing HLA types using SNP data, and relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.

Author
Xiuwen Zheng [aut, cre, cph], Bruce Weir [ctb, ths]
Date of publication
None
Maintainer
Xiuwen Zheng <zhengx@u.washington.edu>
License
GPL-3
Version
1.10.0
URLs

View on Bioconductor

Man pages

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 types
hlaAlleleClass
Class of HLA Type
hlaAlleleDigit
Trim HLA alleles
hlaAlleleSubset
Get a subset of HLA types
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
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
hlaLociInfo
HLA 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
hlaPredMerge
Merge prediction results from multiple HIBAG models
hlaPublish
Finalize a HIBAG model
hlaReport
Format a report
hlaSampleAllele
Get sample IDs from HLA types with a filter
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
predict.hlaAttrBagClass
HIBAG model prediction (in parallel)
print.hlaAttrBagClass
Summarize a "hlaAttrBagClass" or "hlaAttrBagObj" object.
summary.hlaAlleleClass
Summarize a "hlaAlleleClass" or "hlaAASeqClass" object
summary.hlaSNPGenoClass
Summarize a SNP dataset

Files in this package

HIBAG/DESCRIPTION
HIBAG/NAMESPACE
HIBAG/NEWS
HIBAG/R
HIBAG/R/Association.R
HIBAG/R/DataUtilities.R
HIBAG/R/HIBAG.R
HIBAG/R/SeqFormat.R
HIBAG/README.md
HIBAG/build
HIBAG/build/vignette.rds
HIBAG/data
HIBAG/data/HLA_Type_Table.rdata
HIBAG/data/HapMap_CEU_Geno.rdata
HIBAG/inst
HIBAG/inst/CITATION
HIBAG/inst/GPLv3
HIBAG/inst/doc
HIBAG/inst/doc/GeneInfo_hg18.txt
HIBAG/inst/doc/GeneInfo_hg19.txt
HIBAG/inst/doc/GeneInfo_hg20.txt
HIBAG/inst/doc/HIBAG_LICENSE.txt
HIBAG/inst/doc/HIBAG_Tutorial.R
HIBAG/inst/doc/HIBAG_Tutorial.Rmd
HIBAG/inst/doc/HIBAG_Tutorial.html
HIBAG/inst/doc/case_control.txt
HIBAG/inst/extdata
HIBAG/inst/extdata/HapMap_CEU.bed
HIBAG/inst/extdata/HapMap_CEU.bim
HIBAG/inst/extdata/HapMap_CEU.fam
HIBAG/inst/extdata/HapMap_CEU_Chr6.gds
HIBAG/inst/extdata/ModelList.RData
HIBAG/inst/extdata/OutOfBag.RData
HIBAG/inst/extdata/Sequence
HIBAG/inst/extdata/case_control.txt.xz
HIBAG/inst/extdata/v3.22.0
HIBAG/inst/extdata/v3.22.0/FeatureInfo.txt
HIBAG/inst/extdata/v3.22.0/Licence.txt
HIBAG/inst/extdata/v3.22.0/SeqAlign
HIBAG/inst/extdata/v3.22.0/SeqAlign/a_prot.txt.xz
HIBAG/inst/extdata/v3.22.0/SeqAlign/b_prot.txt.xz
HIBAG/inst/extdata/v3.22.0/SeqAlign/c_prot.txt.xz
HIBAG/inst/extdata/v3.22.0/SeqAlign/dpa1_prot.txt.xz
HIBAG/inst/extdata/v3.22.0/SeqAlign/dpb1_prot.txt.xz
HIBAG/inst/extdata/v3.22.0/SeqAlign/dqa1_prot.txt.xz
HIBAG/inst/extdata/v3.22.0/SeqAlign/dqb1_prot.txt.xz
HIBAG/inst/extdata/v3.22.0/SeqAlign/drb1_prot.txt.xz
HIBAG/inst/extdata/v3.22.0/hla_nom_g.txt.xz
HIBAG/inst/extdata/v3.22.0/hla_nom_p.txt.xz
HIBAG/inst/unitTests
HIBAG/man
HIBAG/man/HIBAG-package.Rd
HIBAG/man/HLA_Type_Table.Rd
HIBAG/man/HapMap_CEU_Geno.Rd
HIBAG/man/hlaAASeqClass.Rd
HIBAG/man/hlaAllele.Rd
HIBAG/man/hlaAlleleClass.Rd
HIBAG/man/hlaAlleleDigit.Rd
HIBAG/man/hlaAlleleSubset.Rd
HIBAG/man/hlaAssocTest.Rd
HIBAG/man/hlaAttrBagClass.Rd
HIBAG/man/hlaAttrBagObj.Rd
HIBAG/man/hlaAttrBagging.Rd
HIBAG/man/hlaBED2Geno.Rd
HIBAG/man/hlaCheckAllele.Rd
HIBAG/man/hlaCheckSNPs.Rd
HIBAG/man/hlaClose.Rd
HIBAG/man/hlaCombineAllele.Rd
HIBAG/man/hlaCombineModelObj.Rd
HIBAG/man/hlaCompareAllele.Rd
HIBAG/man/hlaConvSequence.Rd
HIBAG/man/hlaErrMsg.Rd
HIBAG/man/hlaFlankingSNP.Rd
HIBAG/man/hlaGDS2Geno.Rd
HIBAG/man/hlaGeno2PED.Rd
HIBAG/man/hlaGenoAFreq.Rd
HIBAG/man/hlaGenoCombine.Rd
HIBAG/man/hlaGenoLD.Rd
HIBAG/man/hlaGenoMFreq.Rd
HIBAG/man/hlaGenoMRate.Rd
HIBAG/man/hlaGenoMRate_Samp.Rd
HIBAG/man/hlaGenoSubset.Rd
HIBAG/man/hlaGenoSwitchStrand.Rd
HIBAG/man/hlaLociInfo.Rd
HIBAG/man/hlaMakeSNPGeno.Rd
HIBAG/man/hlaModelFiles.Rd
HIBAG/man/hlaModelFromObj.Rd
HIBAG/man/hlaOutOfBag.Rd
HIBAG/man/hlaParallelAttrBagging.Rd
HIBAG/man/hlaPredMerge.Rd
HIBAG/man/hlaPublish.Rd
HIBAG/man/hlaReport.Rd
HIBAG/man/hlaSNPGenoClass.Rd
HIBAG/man/hlaSNPID.Rd
HIBAG/man/hlaSampleAllele.Rd
HIBAG/man/hlaSplitAllele.Rd
HIBAG/man/hlaSubModelObj.Rd
HIBAG/man/hlaUniqueAllele.Rd
HIBAG/man/plot.hlaAttrBagObj.Rd
HIBAG/man/predict.hlaAttrBagClass.Rd
HIBAG/man/print.hlaAttrBagClass.Rd
HIBAG/man/summary.hlaAlleleClass.Rd
HIBAG/man/summary.hlaSNPGenoClass.Rd
HIBAG/src
HIBAG/src/HIBAG.cpp
HIBAG/src/LibHLA.cpp
HIBAG/src/LibHLA.h
HIBAG/tests
HIBAG/tests/runTests.R
HIBAG/vignettes
HIBAG/vignettes/HIBAG_Ref.bib
HIBAG/vignettes/HIBAG_Tutorial.Rmd