seqOptimize {SeqArray} | R Documentation |
Transpose data array or matrix for possibly higher-speed access.
seqOptimize(gdsfn, target=c("chromosome", "by.sample"), format.var=TRUE, cleanup=TRUE, verbose=TRUE)
gdsfn |
the file name of GDS |
target |
"chromosome", "by.sample"; see details |
format.var |
a character vector for selected variable names,
or |
cleanup |
call |
verbose |
if |
"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.
None.
Xiuwen Zheng
# 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")