SeqArray (version 1.12.5)

seqOptimize: Optimize the Storage of Data Array

Description

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

Usage

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

Arguments

gdsfn

a SeqVarGDSClass object

target

"by.sample" -- optimize GDS file for seqApply(..., margin="by.sample")

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

Value

None.

Details

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.

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")

# 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")