snpgdsCreateGenoSet: Create a SNP genotype dataset from a GDS file

In zhengxwen/SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Create a SNP genotype dataset from a GDS file

Description

To create a GDS file of genotypes from a specified GDS file.

Usage

snpgdsCreateGenoSet(src.fn, dest.fn, sample.id=NULL, snp.id=NULL,
    snpfirstdim=NULL, compress.annotation="ZIP_RA.max", compress.geno="",
    verbose=TRUE)

Arguments

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 genotype
compress.geno	the compression method for the variable genotype
verbose	if TRUE, show information

Value

None.

Author(s)

Xiuwen Zheng

See Also

snpgdsCreateGeno, snpgdsCombineGeno

Examples

# 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)

zhengxwen/SNPRelate documentation built on Nov. 19, 2024, 1:02 p.m.