seqExport {SeqArray} | R Documentation

## Export to a GDS File

### Description

Exports to a GDS file with selected samples and variants, which are defined by `seqSetFilter()`.

### Usage

    seqExport(gdsfile, out.fn, info.var=NULL, fmt.var=NULL, samp.var=NULL,
        optimize=TRUE, digest=TRUE, verbose=TRUE)

### Arguments

`gdsfile` | a `SeqVarGDSClass` object
`out.fn` | the file name of output GDS file
`info.var` | characters, the variable name(s) in the INFO field for import; or `NULL` for all variables
`fmt.var` | characters, the variable name(s) in the FORMAT field for import; or `NULL` for all variables
`samp.var` | characters, the variable name(s) in the folder `"sample.annotation"`
`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 md5 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 GDS format with an absolute path.

### Author(s)

Xiuwen Zheng

### See Also

`seqVCF2GDS`

### Examples

    # open the GDS file
    (gds.fn <- seqExampleFileName("gds"))
    (f <- seqOpen(gds.fn))

    # get 'sample.id'
    head(samp.id <- seqGetData(f, "sample.id"))

    # get 'variant.id'
    head(variant.id <- seqGetData(f, "variant.id"))

    set.seed(100)
    # set sample and variant filters
    seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10,12,14,16)])
    seqSetFilter(f, variant.id=sample(variant.id, 100))

    # export
    seqExport(f, "tmp.gds")
    seqExport(f, "tmp.gds", info.var=character())
    seqExport(f, "tmp.gds", fmt.var=character())
    seqExport(f, "tmp.gds", samp.var=character())

    # show file
    (f1 <- seqOpen("tmp.gds")); seqClose(f1)

    # close
    seqClose(f)

    # delete the temporary file
    unlink("tmp.gds")

[Package SeqArray version 1.26.2 Index]