hlaGDS2Geno: Import genotypes from a GDS file
In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

hlaGDS2Geno

R Documentation

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

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 Nov. 24, 2024, 5:24 a.m.