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 1.12.2 Index]