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   { 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)

[Package SNPRelate version 1.14.0 Index]