seqOptimize {SeqArray} | R Documentation

## Optimize the Storage of Data Array

### Description

Transpose data array or matrix for possibly higher-speed access.

### Usage

    seqOptimize(gdsfn, target=c("chromosome", "by.sample"), format.var=TRUE,
        cleanup=TRUE, verbose=TRUE)

### Arguments

`gdsfn` | the file name of GDS
`target` | "chromosome", "by.sample"; see details
`format.var` | a character vector for selected variable names, or `TRUE` for all variables, according to "annotation/format"
`cleanup` | call `link{cleanup.gds}` if `TRUE`
`verbose` | if `TRUE`, show information

### Details

`"chromosome"`: adding or updating two additional nodes '@chrom_rle_val' and '@chrom_rle_len' for faster chromosome indexing, requiring SeqArray>=v1.20.0.

`"by.sample"`: optimizing GDS file for `seqApply(..., margin="by.sample")`. Warning: optimizing GDS file for reading data by sample may increase file size by up to 2X as genotype data and all format data are duplicated.

### Value

None.

### Author(s)

Xiuwen Zheng

### See Also

`seqGetData`, `seqApply`

### Examples

    # the file name of VCF
    (vcf.fn <- seqExampleFileName("vcf"))
    # or vcf.fn <- "C:/YourFolder/Your_VCF_File.vcf"

    # convert
    seqVCF2GDS(vcf.fn, "tmp.gds", storage.option="ZIP_RA")

    # prepare data for the SeqVarTools package
    seqOptimize("tmp.gds", target="by.sample")

    # list the structure of GDS variables
    (f <- seqOpen("tmp.gds"))
    # close
    seqClose(f)

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

[Package SeqArray version 1.22.6 Index]