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.

AuthorXiuwen Zheng [aut, cre, cph], Bruce Weir [ctb, ths]
Date of publicationNone
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseGPL-3
Version1.10.0
http://www.biostat.washington.edu/~bsweir/HIBAG/, http://github.com/zhengxwen/HIBAG

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

Functions

HapMap_CEU_Geno Man page
HIBAG Man page
HIBAG-package Man page
hlaAASeqClass Man page
hlaAllele Man page
hlaAlleleClass Man page
hlaAlleleDigit Man page
hlaAlleleSubset Man page
hlaAssocTest Man page
hlaAssocTest.hlaAASeqClass Man page
hlaAssocTest.hlaAlleleClass Man page
hlaAttrBagClass Man page
hlaAttrBagging Man page
hlaAttrBagObj Man page
hlaBED2Geno Man page
hlaCheckAllele Man page
hlaCheckSNPs Man page
hlaClose Man page
hlaCombineAllele Man page
hlaCombineModelObj Man page
hlaCompareAllele Man page
hlaConvSequence Man page
hlaErrMsg Man page
hlaFlankingSNP Man page
hlaGDS2Geno Man page
hlaGeno2PED Man page
hlaGenoAFreq Man page
hlaGenoCombine Man page
hlaGenoLD Man page
hlaGenoMFreq Man page
hlaGenoMRate Man page
hlaGenoMRate_Samp Man page
hlaGenoSubset Man page
hlaGenoSwitchStrand Man page
hlaLociInfo Man page
hlaMakeSNPGeno Man page
hlaModelFiles Man page
hlaModelFromObj Man page
hlaModelToObj Man page
hlaOutOfBag Man page
hlaParallelAttrBagging Man page
hlaPredict Man page
hlaPredMerge Man page
hlaPublish Man page
hlaReport Man page
hlaSampleAllele Man page
hlaSNPGenoClass Man page
hlaSNPID Man page
hlaSplitAllele Man page
hlaSubModelObj Man page
HLA_Type_Table Man page
hlaUniqueAllele Man page
plot.hlaAttrBagClass Man page
plot.hlaAttrBagObj Man page
predict.hlaAttrBagClass Man page
print.hlaAttrBagClass Man page
print.hlaAttrBagObj Man page
summary.hlaAASeqClass Man page
summary.hlaAlleleClass Man page
summary.hlaAttrBagClass Man page
summary.hlaAttrBagObj Man page
summary.hlaSNPGenoClass Man page

Files

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

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