hlaSubModelObj: Get a subset of individual classifiers

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

Description

Get the first n individual classifiers.

Usage

hlaSubModelObj(obj, n)

Arguments

obj	an object of hlaAttrBagObj
n	an integer, get the first n individual classifiers

Value

Return an object of hlaAttrBagObj.

Author(s)

Xiuwen Zheng

See Also

hlaAttrBagging

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 <- "C"
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")

# training genotypes
region <- 50   # kb
snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position,
	hla.id, region*1000, assembly="hg19")
train.geno <- hlaGenoSubset(HapMap_CEU_Geno,
	snp.sel = match(snpid, HapMap_CEU_Geno$snp.id))

# train a HIBAG model
set.seed(1000)
# please use "nclassifier=100" when you use HIBAG for real data
model <- hlaAttrBagging(hla, train.geno, nclassifier=2, verbose.detail=TRUE)
mobj <- hlaModelToObj(model)
summary(mobj)

newmobj <- hlaSubModelObj(mobj, 1)
summary(newmobj)

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