seqExport {SeqArray} | R Documentation |
Exports to a GDS file with selected samples and variants, which are defined
by seqSetFilter()
.
seqExport(gdsfile, out.fn, info.var=NULL, fmt.var=NULL, samp.var=NULL, optimize=TRUE, digest=TRUE, verbose=TRUE)
gdsfile |
a |
out.fn |
the file name of output GDS file |
info.var |
characters, the variable name(s) in the INFO field
for import; or |
fmt.var |
characters, the variable name(s) in the FORMAT field
for import; or |
samp.var |
characters, the variable name(s) in the folder
|
optimize |
if |
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 |
Return the file name of GDS format with an absolute path.
Xiuwen Zheng
# open the GDS file (gds.fn <- seqExampleFileName("gds")) (f <- seqOpen(gds.fn)) # get 'sample.id' head(samp.id <- seqGetData(f, "sample.id")) # get 'variant.id' head(variant.id <- seqGetData(f, "variant.id")) set.seed(100) # set sample and variant filters seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10,12,14,16)]) seqSetFilter(f, variant.id=sample(variant.id, 100)) # export seqExport(f, "tmp.gds") seqExport(f, "tmp.gds", info.var=character()) seqExport(f, "tmp.gds", fmt.var=character()) seqExport(f, "tmp.gds", samp.var=character()) # show file (f1 <- seqOpen("tmp.gds")); seqClose(f1) # close seqClose(f) # delete the temporary file unlink("tmp.gds")