snpgdsCreateGenoSet {SNPRelate}R Documentation

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    { FStr8 279 ZIP(23.10%) }
# |--+ snp.id   { Int32 9088 ZIP(34.76%) }
# |--+ snp.rs.id    { FStr8 9088 ZIP(42.66%) }
# |--+ snp.position { Int32 9088 ZIP(94.73%) }
# |--+ snp.chromosome   { UInt8 9088 ZIP(0.94%) } *
# |--+ snp.allele   { FStr8 9088 ZIP(14.45%) }
# |--+ genotype { Bit2 9088x279 } *
# |--+ sample.annot [ data.frame ] *
# |  |--+ sample.id { FStr8 279 ZIP(23.10%) }
# |  |--+ family.id { FStr8 279 ZIP(28.37%) }
# |  |--+ geneva.id { Int32 279 ZIP(80.29%) }
# |  |--+ father.id { FStr8 279 ZIP(12.98%) }
# |  |--+ mother.id { FStr8 279 ZIP(12.86%) }
# |  |--+ plate.id  { FStr8 279 ZIP(1.29%) }
# |  |--+ sex   { FStr8 279 ZIP(28.32%) }
# |  |--+ pop.group { FStr8 279 ZIP(7.89%) }

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    { VStr8 279 ZIP(29.89%) }
# |--+ snp.id   { Int32 6547 ZIP(34.89%) }
# |--+ snp.rs.id    { VStr8 6547 ZIP(40.52%) }
# |--+ snp.position { Int32 6547 ZIP(94.85%) }
# |--+ snp.chromosome   { Int32 6547 ZIP(0.41%) }
# |--+ snp.allele   { VStr8 6547 ZIP(11.51%) }
# |--+ genotype { Bit2 6547x279 } *

# close the file
snpgdsClose(gfile)


unlink("test.gds", force=TRUE)
[Package SNPRelate version 1.10.2 Index]