hlaGDS2Geno {HIBAG} | R Documentation

## 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), "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)

[Package HIBAG version 1.18.1 Index]