seqSNP2GDS {SeqArray} | R Documentation

## Convert SNPRelate Format to SeqArray Format

### Description

Converts a SNP GDS file to a SeqArray GDS file.

### Usage

    seqSNP2GDS(gds.fn, out.fn, storage.option="LZMA_RA", major.ref=TRUE,
        ds.type=c("packedreal16", "float", "double"), optimize=TRUE, digest=TRUE,
        verbose=TRUE)

### Arguments

`gds.fn` | the file name of SNP format
`out.fn` | the file name, output a file of SeqArray format
`storage.option` | specify the storage and compression options, `"LZMA_RA"` to use LZMA compression algorithm with higher compression ratio compared to `"ZIP_RA"`
`major.ref` | if TRUE, use the major allele as a reference allele; otherwise, use A allele in SNP GDS file as a reference allele
`ds.type` | applicable when import dosages, the data type for storing dosages; see `add.gdsn`; `ds.type="packedreal16"` by default
`optimize` | if `TRUE`, optimize the access efficiency by calling `cleanup.gds`
`digest` | a logical value (TRUE/FALSE) or a character ("md5", "sha1", "sha256", "sha384" or "sha512"); add hash codes to the GDS file if TRUE or a digest algorithm is specified
`verbose` | if `TRUE`, show information

### Value

Return the file name of SeqArray file with an absolute path. If the input file is genotype dosage, the dosage matrix is stored in the node `annotation/format/DS` with the estimated dosage of alternative alleles. Any value less than 0 or greater than 2 will be replaced by NaN.

### Author(s)

Xiuwen Zheng

### See Also

`seqGDS2SNP`, `seqVCF2GDS`, `seqGDS2VCF`, `seqBED2GDS`

### Examples

    library(SNPRelate)

    # the GDS file
    gds.fn <- snpgdsExampleFileName()

    seqSNP2GDS(gds.fn, "tmp.gds")

    seqSummary("tmp.gds")

    # remove the temporary file
    unlink("tmp.gds", force=TRUE)

[Package SeqArray version 1.27.15 Index]