HIBAG (version 1.8.3)

hlaGDS2Geno: Convert from SNP GDS format

Description

To convert a SNP GDS file to an object of hlaSNPGenoClass.

Usage

hlaGDS2Geno(gds.fn, rm.invalid.allele=FALSE, import.chr="xMHC", assembly="auto", verbose=TRUE)

Arguments

gds.fn

the SNP GDS file used by the SNPRelate package

rm.invalid.allele

if TRUE, remove SNPs with invalid alleles

import.chr

the chromosome, "1" .. "22", "X", "Y", "XY", "MT", "xMHC", or "", where "xMHC" implies the extended MHC on chromosome 6, and "" for all SNPs

assembly

the human genome reference: "hg18", "hg19" (default), "hg20"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning

verbose

if TRUE, show information

Value

Return an object of hlaSNPGenoClass.

See Also

hlaGeno2PED, hlaBED2Geno

Examples

# Import a SNP GDS file
fn <- system.file("extdata", "HapMap_CEU_Chr6.gds", package="HIBAG")

geno <- hlaGDS2Geno(fn, assembly="hg18",
    rm.invalid.allele=TRUE, import.chr="6")

summary(geno)