HIBAG: HIBAG -- HLA Genotype Imputation with Attribute Bagging

HIBAG is a state of the art software package for imputing HLA types using SNP data, and it uses the R statistical programming language. 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], Bruce Weir [ctb, ths]
Date of publication
2014-12-25 11:33:28
Maintainer
Xiuwen Zheng <zhengx@u.washington.edu>
License
GPL-3
Version
1.2.5
URLs

View on R-Forge

Man pages

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

Files in this package

HIBAG/DESCRIPTION
HIBAG/NAMESPACE
HIBAG/NEWS
HIBAG/R
HIBAG/R/HIBAG.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/HIBAG_LICENSE
HIBAG/inst/doc
HIBAG/inst/doc/HIBAG_Tutorial.Rnw
HIBAG/inst/doc/HIBAG_Tutorial.pdf
HIBAG/inst/extdata
HIBAG/inst/extdata/HapMap_CEU.bed
HIBAG/inst/extdata/HapMap_CEU.bim
HIBAG/inst/extdata/HapMap_CEU.fam
HIBAG/man
HIBAG/man/HIBAG-package.Rd
HIBAG/man/HLA_Type_Table.Rd
HIBAG/man/HapMap_CEU_Geno.Rd
HIBAG/man/hlaAllele.Rd
HIBAG/man/hlaAlleleClass.Rd
HIBAG/man/hlaAlleleDigit.Rd
HIBAG/man/hlaAlleleSubset.Rd
HIBAG/man/hlaAttrBagClass.Rd
HIBAG/man/hlaAttrBagObj.Rd
HIBAG/man/hlaAttrBagging.Rd
HIBAG/man/hlaBED2Geno.Rd
HIBAG/man/hlaCheckSNPs.Rd
HIBAG/man/hlaClose.Rd
HIBAG/man/hlaCombineAllele.Rd
HIBAG/man/hlaCombineModelObj.Rd
HIBAG/man/hlaCompareAllele.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/hlaHaplo2Geno.Rd
HIBAG/man/hlaHaploSubset.Rd
HIBAG/man/hlaLociInfo.Rd
HIBAG/man/hlaMakeSNPGeno.Rd
HIBAG/man/hlaMakeSNPHaplo.Rd
HIBAG/man/hlaModelFiles.Rd
HIBAG/man/hlaModelFromObj.Rd
HIBAG/man/hlaModelToObj.Rd
HIBAG/man/hlaOutOfBag.Rd
HIBAG/man/hlaParallelAttrBagging.Rd
HIBAG/man/hlaPredMerge.Rd
HIBAG/man/hlaPublish.Rd
HIBAG/man/hlaReport.Rd
HIBAG/man/hlaResource.Rd
HIBAG/man/hlaSNPGenoClass.Rd
HIBAG/man/hlaSNPHaploClass.Rd
HIBAG/man/hlaSNPID.Rd
HIBAG/man/hlaSampleAllele.Rd
HIBAG/man/hlaSplitAllele.Rd
HIBAG/man/hlaSubModelObj.Rd
HIBAG/man/hlaUniqueAllele.Rd
HIBAG/man/plot.hlaAttrBagClass.Rd
HIBAG/man/plot.hlaAttrBagObj.Rd
HIBAG/man/predict.hlaAttrBagClass.Rd
HIBAG/man/print.hlaAttrBagClass.Rd
HIBAG/man/print.hlaAttrBagObj.Rd
HIBAG/man/summary.hlaAlleleClass.Rd
HIBAG/man/summary.hlaAttrBagClass.Rd
HIBAG/man/summary.hlaAttrBagObj.Rd
HIBAG/man/summary.hlaSNPGenoClass.Rd
HIBAG/man/summary.hlaSNPHaploClass.Rd
HIBAG/src
HIBAG/src/HIBAG.cpp
HIBAG/src/LibHLA.cpp
HIBAG/src/LibHLA.h
HIBAG/vignettes
HIBAG/vignettes/HIBAG_Ref.bib
HIBAG/vignettes/HIBAG_Tutorial.Rnw