seqOptimize {SeqArray} | R Documentation |
Transpose data array or matrix for possibly higher-speed access.
seqOptimize(gdsfn, target=c("by.sample"), format.var=TRUE, cleanup=TRUE, verbose=TRUE)
gdsfn |
a |
target |
"by.sample" – optimize GDS file for
|
format.var |
a character vector for selected variable names,
or |
cleanup |
call |
verbose |
if |
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")