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.

AuthorXiuwen Zheng [aut, cre], Bruce Weir [ctb, ths]
Date of publication2014-12-25 11:33:28
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseGPL-3
Version1.2.5
http://www.biostat.washington.edu/~bsweir/HIBAG/, http://github.com/zhengxwen/HIBAG

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

Functions

HapMap_CEU_Geno Man page
HIBAG Man page
HIBAG-package Man page
hlaAllele Man page
hlaAlleleClass Man page
hlaAlleleDigit Man page
hlaAlleleSubset Man page
hlaAttrBagClass Man page
hlaAttrBagging Man page
hlaAttrBagObj Man page
hlaBED2Geno Man page
hlaCheckSNPs Man page
hlaClose Man page
hlaCombineAllele Man page
hlaCombineModelObj Man page
hlaCompareAllele 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
hlaHaplo2Geno Man page
hlaHaploSubset Man page
hlaLociInfo Man page
hlaMakeSNPGeno Man page
hlaMakeSNPHaplo Man page
hlaModelFiles Man page
hlaModelFromObj Man page
hlaModelToObj Man page
hlaOutOfBag Man page
hlaParallelAttrBagging Man page
hlaPredMerge Man page
hlaPublish Man page
hlaReport Man page
hlaResource Man page
hlaSampleAllele Man page
hlaSNPGenoClass Man page
hlaSNPHaploClass 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.hlaAlleleClass Man page
summary.hlaAttrBagClass Man page
summary.hlaAttrBagObj Man page
summary.hlaSNPGenoClass Man page
summary.hlaSNPHaploClass Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/HIBAG.r
README.md
build
build/vignette.rds
data
data/HLA_Type_Table.rdata
data/HapMap_CEU_Geno.rdata
inst
inst/CITATION
inst/GPLv3
inst/HIBAG_LICENSE
inst/doc
inst/doc/HIBAG_Tutorial.Rnw
inst/doc/HIBAG_Tutorial.pdf
inst/extdata
inst/extdata/HapMap_CEU.bed
inst/extdata/HapMap_CEU.bim
inst/extdata/HapMap_CEU.fam
man
man/HIBAG-package.Rd man/HLA_Type_Table.Rd man/HapMap_CEU_Geno.Rd man/hlaAllele.Rd man/hlaAlleleClass.Rd man/hlaAlleleDigit.Rd man/hlaAlleleSubset.Rd man/hlaAttrBagClass.Rd man/hlaAttrBagObj.Rd man/hlaAttrBagging.Rd man/hlaBED2Geno.Rd man/hlaCheckSNPs.Rd man/hlaClose.Rd man/hlaCombineAllele.Rd man/hlaCombineModelObj.Rd man/hlaCompareAllele.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/hlaHaplo2Geno.Rd man/hlaHaploSubset.Rd man/hlaLociInfo.Rd man/hlaMakeSNPGeno.Rd man/hlaMakeSNPHaplo.Rd man/hlaModelFiles.Rd man/hlaModelFromObj.Rd man/hlaModelToObj.Rd man/hlaOutOfBag.Rd man/hlaParallelAttrBagging.Rd man/hlaPredMerge.Rd man/hlaPublish.Rd man/hlaReport.Rd man/hlaResource.Rd man/hlaSNPGenoClass.Rd man/hlaSNPHaploClass.Rd man/hlaSNPID.Rd man/hlaSampleAllele.Rd man/hlaSplitAllele.Rd man/hlaSubModelObj.Rd man/hlaUniqueAllele.Rd man/plot.hlaAttrBagClass.Rd man/plot.hlaAttrBagObj.Rd man/predict.hlaAttrBagClass.Rd man/print.hlaAttrBagClass.Rd man/print.hlaAttrBagObj.Rd man/summary.hlaAlleleClass.Rd man/summary.hlaAttrBagClass.Rd man/summary.hlaAttrBagObj.Rd man/summary.hlaSNPGenoClass.Rd man/summary.hlaSNPHaploClass.Rd
src
src/HIBAG.cpp
src/LibHLA.cpp
src/LibHLA.h
vignettes
vignettes/HIBAG_Ref.bib
vignettes/HIBAG_Tutorial.Rnw

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