hlaGDS2Geno: Convert from SNP GDS format

In HIBAG: HLA Genotype Imputation with Attribute Bagging

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), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning
verbose	if TRUE, show information

Value

Return an object of hlaSNPGenoClass.

Author(s)

Xiuwen Zheng

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)

HIBAG documentation built on March 24, 2021, 6 p.m.