hlaGeno2PED: Convert to PLINK PED format

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Convert to PLINK PED format

Description

Convert an object of hlaSNPGenoClass to a file of PLINK PED format.

Usage

hlaGeno2PED(geno, out.fn)

Arguments

geno	a genotype object of hlaSNPGenoClass
out.fn	the file name of output ped file

Details

Two files ".map" and ".ped" are created.

Value

None.

Author(s)

Xiuwen Zheng

See Also

hlaBED2Geno

Examples

# 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="")],
    max.resolution="4-digit", locus=hla.id, assembly="hg19")

# training genotypes
region <- 500   # 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))

hlaGeno2PED(train.geno, "test")


# delete the temporary files
unlink(c("test.map", "test.ped"), force=TRUE)

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