snpgdsCombineGeno {SNPRelate} | R Documentation

## Merge SNP datasets

### Description

To merge GDS files of SNP genotypes into a single GDS file

### Usage

    snpgdsCombineGeno(gds.fn, out.fn, sample.id=NULL, snpobj=NULL,
        name.prefix=NULL, snpfirstdim=TRUE, compress.annotation="ZIP_RA.MAX",
        compress.geno="", other.vars=NULL, verbose=TRUE)

### Arguments

`gds.fn` | a list of SNP GDS files to be merged
`out.fn` | the name of output GDS file
`sample.id` | NULL, or a list. If it is a list, specify sample ids for each SNP GDS file
`snpobj` | specify a `snpgdsSNPListClass` object, used for strand switch; if NULL, the strand information of the first SNP GDS file is used
`name.prefix` | NULL, a character vector (added to sample ids for each GDS file)
`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`
`other.vars` | a list object storing other variables
`verbose` | if TRUE, show information

### Details

The typical variables specified in `other.vars` are “sample.annot” and “snp.annot”, which are data.frame objects.

WARNING: the functionality of `snpgdsCombineGeno()` is limited.

### Value

None.

### Author(s)

Xiuwen Zheng

### See Also

`snpgdsCreateGeno`, `snpgdsCreateGenoSet`

### Examples

    # get the file name of a gds file
    fn <- snpgdsExampleFileName()

    # combine
    snpgdsCombineGeno(c(fn, fn), "test.gds")

    snpgdsSummary("test.gds")

[Package SNPRelate version 1.12.2 Index]