snpgdsCreateGenoSet {SNPRelate} | R Documentation |
To create a GDS file of genotypes from a specified GDS file.
snpgdsCreateGenoSet(src.fn, dest.fn, sample.id=NULL, snp.id=NULL, snpfirstdim=NULL, compress.annotation="ZIP_RA.max", compress.geno="", verbose=TRUE)
src.fn |
the file name of a specified GDS file |
dest.fn |
the file name of output GDS file |
sample.id |
a vector of sample id specifying selected samples; if NULL, all samples are used |
snp.id |
a vector of snp id specifying selected SNPs; if NULL, all SNPs are used |
snpfirstdim |
if TRUE, genotypes are stored in the individual-major mode, (i.e, list all SNPs for the first individual, and then list all SNPs for the second individual, etc) |
compress.annotation |
the compression method for the variables except
|
compress.geno |
the compression method for the variable
|
verbose |
if TRUE, show information |
None.
Xiuwen Zheng
snpgdsCreateGeno
, snpgdsCombineGeno
# open an example dataset (HapMap) (genofile <- snpgdsOpen(snpgdsExampleFileName())) # + [ ] * # |--+ sample.id { VStr8 279 ZIP(29.9%), 679B } # |--+ snp.id { Int32 9088 ZIP(34.8%), 12.3K } # |--+ snp.rs.id { VStr8 9088 ZIP(40.1%), 36.2K } # |--+ snp.position { Int32 9088 ZIP(94.7%), 33.6K } # |--+ snp.chromosome { UInt8 9088 ZIP(0.94%), 85B } * # |--+ snp.allele { VStr8 9088 ZIP(11.3%), 4.0K } # |--+ genotype { Bit2 279x9088, 619.0K } * # \--+ sample.annot [ data.frame ] * # |--+ family.id { VStr8 279 ZIP(34.4%), 514B } # |--+ father.id { VStr8 279 ZIP(31.5%), 220B } # |--+ mother.id { VStr8 279 ZIP(30.9%), 214B } # |--+ sex { VStr8 279 ZIP(17.0%), 95B } # \--+ pop.group { VStr8 279 ZIP(6.18%), 69B } set.seed(1000) snpset <- unlist(snpgdsLDpruning(genofile)) length(snpset) # 6547 # close the file snpgdsClose(genofile) snpgdsCreateGenoSet(snpgdsExampleFileName(), "test.gds", snp.id=snpset) #################################################### # check (gfile <- snpgdsOpen("test.gds")) # + [ ] * # |--+ sample.id { Str8 279 ZIP_ra(31.2%), 715B } # |--+ snp.id { Int32 6547 ZIP_ra(34.9%), 8.9K } # |--+ snp.rs.id { Str8 6547 ZIP_ra(41.5%), 27.1K } # |--+ snp.position { Int32 6547 ZIP_ra(94.9%), 24.3K } # |--+ snp.chromosome { Int32 6547 ZIP_ra(0.45%), 124B } # |--+ snp.allele { Str8 6547 ZIP_ra(11.5%), 3.0K } # \--+ genotype { Bit2 279x6547, 446.0K } * # close the file snpgdsClose(gfile) unlink("test.gds", force=TRUE)