hlaGDS2Geno: Import genotypes from a GDS file

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Import genotypes from a GDS file

Description

To convert a SNPRelate or SeqArray 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	a file name for the GDS file defined in the SNPRelate or SeqArray package
rm.invalid.allele	if TRUE, remove SNPs with non-standard alleles (except A,G,C,T)
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)

summary(geno)

zhengxwen/HIBAG documentation built on April 16, 2024, 8:41 a.m.