seqTranspose: Transpose Data Array

In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Transpose Data Array

Description

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

Usage

seqTranspose(gdsfile, var.name, compress=NULL, digest=TRUE, verbose=TRUE)

Arguments

gdsfile	a SeqVarGDSClass object
var.name	the variable name with '/' as a separator
compress	the compression option used in add.gdsn; or determine automatically if NULL
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

Details

It is designed for possibly higher-speed access. More details will be provided in the future version.

Value

None.

Author(s)

Xiuwen Zheng

See Also

seqGetData, seqApply

Examples

# the VCF file
(vcf.fn <- seqExampleFileName("vcf"))

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

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

seqTranspose(f, "genotype/data")
f

# the original array
index.gdsn(f, "genotype/data")
# the transposed array
index.gdsn(f, "genotype/~data")

# close
seqClose(f)

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

zhengxwen/SeqArray documentation built on Nov. 19, 2024, 1:04 p.m.