HIBAG: HLA Genotype Imputation with Attribute Bagging
Version 1.12.0

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]
Bioconductor views Genetics StatisticalMethod
Date of publicationNone
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseGPL-3
Version1.12.0
URL http://www.biostat.washington.edu/~bsweir/HIBAG/ http://github.com/zhengxwen/HIBAG
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("HIBAG")

Getting started

Package overview
README.md
HIBAG -- an R Package for HLA Genotype Imputation with Attribute Bagging

Popular 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
hlaAssocTest: Statistical Association Tests
hlaCheckSNPs: Check the SNP predictors in a HIBAG model
hlaConvSequence: Conversion From HLA Alleles to Amino Acid Sequences
hlaSNPGenoClass: The class of SNP genotypes
See all...

All man pages Function index File listing

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

DynamicClusterCall Source code
HIBAG Man page
HIBAG-package Man page
HLA_Type_Table Man page
HapMap_CEU_Geno Man page
assoc_show Source code
feature Source code
gcode Source code
hlaAASeqClass Man page
hlaAllele Man page Source code
hlaAlleleClass Man page
hlaAlleleDigit Man page Source code
hlaAlleleSubset Man page Source code
hlaAssocTest Man page Source code
hlaAssocTest.hlaAASeqClass Man page Source code
hlaAssocTest.hlaAlleleClass Man page Source code
hlaAttrBagClass Man page
hlaAttrBagObj Man page
hlaAttrBagging Man page Source code
hlaBED2Geno Man page Source code
hlaCheckAllele Man page Source code
hlaCheckSNPs Man page Source code
hlaClose Man page Source code
hlaCombineAllele Man page Source code
hlaCombineModelObj Man page Source code
hlaCompareAllele Man page Source code
hlaConvSequence Man page Source code
hlaErrMsg Man page Source code
hlaFlankingSNP Man page Source code
hlaGDS2Geno Man page Source code
hlaGeno2PED Man page Source code
hlaGenoAFreq Man page Source code
hlaGenoCombine Man page Source code
hlaGenoLD Man page Source code
hlaGenoMFreq Man page Source code
hlaGenoMRate Man page Source code
hlaGenoMRate_Samp Man page Source code
hlaGenoSubset Man page Source code
hlaGenoSwitchStrand Man page Source code
hlaLociInfo Man page Source code
hlaMakeSNPGeno Man page Source code
hlaModelFiles Man page Source code Source code
hlaModelFromObj Man page Source code
hlaModelToObj Man page Source code
hlaOutOfBag Man page Source code Source code
hlaParallelAttrBagging Man page Source code
hlaPredMerge Man page Source code
hlaPredict Man page Source code
hlaPublish Man page Source code
hlaReport Man page Source code
hlaSNPGenoClass Man page
hlaSNPID Man page Source code
hlaSampleAllele Man page Source code
hlaSplitAllele Man page Source code
hlaSubModelObj Man page Source code
hlaUniqueAllele Man page Source code
hla_assembly Source code
hla_gene_name_string Source code
matrix_sequence Source code
onAttach Source code
pcode Source code
plot.hlaAttrBagClass Man page Source code
plot.hlaAttrBagObj Man page Source code
plural Source code
predict.hlaAttrBagClass Man page Source code
print.hlaAttrBagClass Man page Source code
print.hlaAttrBagObj Man page Source code
protein Source code
strbp Source code
subset Source code
summary.hlaAASeqClass Man page Source code
summary.hlaAlleleClass Man page Source code
summary.hlaAttrBagClass Man page Source code
summary.hlaAttrBagObj Man page Source code
summary.hlaSNPGenoClass Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Association.R
R/DataUtilities.R
R/HIBAG.R
R/SeqFormat.R
README.md
build
build/vignette.rds
data
data/HLA_Type_Table.rdata
data/HapMap_CEU_Geno.rdata
inst
inst/CITATION
inst/GPLv3
inst/doc
inst/doc/GeneInfo_hg18.txt
inst/doc/GeneInfo_hg19.txt
inst/doc/GeneInfo_hg38.txt
inst/doc/HIBAG_LICENSE.txt
inst/doc/HIBAG_Tutorial.R
inst/doc/HIBAG_Tutorial.Rmd
inst/doc/HIBAG_Tutorial.html
inst/doc/case_control.txt
inst/extdata
inst/extdata/HapMap_CEU.bed
inst/extdata/HapMap_CEU.bim
inst/extdata/HapMap_CEU.fam
inst/extdata/HapMap_CEU_Chr6.gds
inst/extdata/ModelList.RData
inst/extdata/OutOfBag.RData
inst/extdata/Sequence
inst/extdata/case_control.txt.xz
inst/extdata/v3.22.0
inst/extdata/v3.22.0/FeatureInfo.txt
inst/extdata/v3.22.0/Licence.txt
inst/extdata/v3.22.0/SeqAlign
inst/extdata/v3.22.0/SeqAlign/a_prot.txt.xz
inst/extdata/v3.22.0/SeqAlign/b_prot.txt.xz
inst/extdata/v3.22.0/SeqAlign/c_prot.txt.xz
inst/extdata/v3.22.0/SeqAlign/dpa1_prot.txt.xz
inst/extdata/v3.22.0/SeqAlign/dpb1_prot.txt.xz
inst/extdata/v3.22.0/SeqAlign/dqa1_prot.txt.xz
inst/extdata/v3.22.0/SeqAlign/dqb1_prot.txt.xz
inst/extdata/v3.22.0/SeqAlign/drb1_prot.txt.xz
inst/extdata/v3.22.0/hla_nom_g.txt.xz
inst/extdata/v3.22.0/hla_nom_p.txt.xz
inst/unitTests
man
man/HIBAG-package.Rd
man/HLA_Type_Table.Rd
man/HapMap_CEU_Geno.Rd
man/hlaAASeqClass.Rd
man/hlaAllele.Rd
man/hlaAlleleClass.Rd
man/hlaAlleleDigit.Rd
man/hlaAlleleSubset.Rd
man/hlaAssocTest.Rd
man/hlaAttrBagClass.Rd
man/hlaAttrBagObj.Rd
man/hlaAttrBagging.Rd
man/hlaBED2Geno.Rd
man/hlaCheckAllele.Rd
man/hlaCheckSNPs.Rd
man/hlaClose.Rd
man/hlaCombineAllele.Rd
man/hlaCombineModelObj.Rd
man/hlaCompareAllele.Rd
man/hlaConvSequence.Rd
man/hlaErrMsg.Rd
man/hlaFlankingSNP.Rd
man/hlaGDS2Geno.Rd
man/hlaGeno2PED.Rd
man/hlaGenoAFreq.Rd
man/hlaGenoCombine.Rd
man/hlaGenoLD.Rd
man/hlaGenoMFreq.Rd
man/hlaGenoMRate.Rd
man/hlaGenoMRate_Samp.Rd
man/hlaGenoSubset.Rd
man/hlaGenoSwitchStrand.Rd
man/hlaLociInfo.Rd
man/hlaMakeSNPGeno.Rd
man/hlaModelFiles.Rd
man/hlaModelFromObj.Rd
man/hlaOutOfBag.Rd
man/hlaParallelAttrBagging.Rd
man/hlaPredMerge.Rd
man/hlaPublish.Rd
man/hlaReport.Rd
man/hlaSNPGenoClass.Rd
man/hlaSNPID.Rd
man/hlaSampleAllele.Rd
man/hlaSplitAllele.Rd
man/hlaSubModelObj.Rd
man/hlaUniqueAllele.Rd
man/plot.hlaAttrBagObj.Rd
man/predict.hlaAttrBagClass.Rd
man/print.hlaAttrBagClass.Rd
man/summary.hlaAlleleClass.Rd
man/summary.hlaSNPGenoClass.Rd
src
src/HIBAG.cpp
src/LibHLA.cpp
src/LibHLA.h
tests
tests/runTests.R
vignettes
vignettes/HIBAG_Ref.bib
vignettes/HIBAG_Tutorial.Rmd
HIBAG documentation built on May 20, 2017, 10:24 p.m.

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