hlaModelFromObj: Conversion between the in-memory model and the object that...

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Conversion between the in-memory model and the object that can be saved in a file

Description

Build a model hlaAttrBagClass from an object of hlaAttrBagObj which is stored in an R object file, or convert hlaAttrBagClass to hlaAttrBagObj.

Usage

hlaModelFromObj(obj)
hlaModelToObj(model)

Arguments

obj	an object of hlaAttrBagObj
model	an object of hlaAttrBagClass

Value

hlaModelFromObj returns hlaAttrBagClass, and hlaModelToObj returns hlaAttrBagObj.

Author(s)

Xiuwen Zheng

See Also

hlaAttrBagging

Examples

# make a "hlaAlleleClass" object
hla.id <- "DQB1"
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 <- 100   # 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)
model <- hlaAttrBagging(hla, train.geno, nclassifier=2)
print(model)

mobj <- hlaModelToObj(model)

is(model)
is(mobj)


# close the HIBAG model explicitly
hlaClose(model)

zhengxwen/HIBAG documentation built on Nov. 24, 2024, 5:24 a.m.