seqTranspose: Transpose Data Array
In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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

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

None.

Xiuwen Zheng

seqGetData, seqApply

# 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")