hlaCombineModelObj: Combine two HIBAG models together

In HIBAG: HIBAG -- HLA Genotype Imputation with Attribute Bagging

Description

Merge two objects of hlaAttrBagObj together, which is useful for building an ensemble model in parallel.

Usage

hlaCombineModelObj(obj1, obj2)

Arguments

obj1	an object of hlaAttrBagObj
obj2	an object of hlaAttrBagObj

Value

Return an object of hlaAttrBagObj.

Author(s)

Xiuwen Zheng

See Also

hlaAttrBagging, hlaModelFiles

Examples

# load HLA types and SNP genotypes
data(HLA_Type_Table, package="HIBAG")
data(HapMap_CEU_Geno, package="HIBAG")

# make a "hlaAlleleClass" object
hla.id <- "A"
hla <- hlaAllele(HLA_Type_Table$sample.id,
	H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")],
	H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")],
	locus=hla.id, assembly="hg19")

# SNP predictors within the flanking region on each side
region <- 500   # kb
snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position,
	hla.id, region*1000, assembly="hg19")
length(snpid)  # 275

# training genotypes
train.geno <- hlaGenoSubset(HapMap_CEU_Geno,
	snp.sel = match(snpid, HapMap_CEU_Geno$snp.id))

# train a HIBAG model
set.seed(100)
m1 <- hlaAttrBagging(hla, train.geno, nclassifier=1)
m2 <- hlaAttrBagging(hla, train.geno, nclassifier=1)

m1.obj <- hlaModelToObj(m1)
m2.obj <- hlaModelToObj(m2)

m.obj <- hlaCombineModelObj(m1.obj, m2.obj)
summary(m.obj)

HIBAG documentation built on May 2, 2019, 4:50 p.m.