seqOptimize: Optimize the Storage of Data Array
In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

seqOptimize

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

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")

zhengxwen/SeqArray documentation built on Dec. 14, 2024, 8:36 p.m.