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, method=c("position", "exact"),
        compress.annotation="ZIP_RA.MAX", compress.geno="",
        same.strand=FALSE, snpfirstdim=FALSE, verbose=TRUE)

### Arguments

`gds.fn` | a character vector of GDS file names to be merged
`out.fn` | the name of output GDS file
`method` | `"exact"`: matching by all snp.id, chromosomes, positions and alleles; `"position"`: matching by chromosomes and positions
`compress.annotation` | the compression method for the variables except `genotype`
`compress.geno` | the compression method for the variable `genotype`
`same.strand` | if TRUE, assuming the alleles on the same strand
`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)
`verbose` | if TRUE, show information

### Details

This function calls `snpgdsSNPListIntersect` internally to determine the common SNPs. Allele definitions are taken from the first GDS file.

### Value

None.

### Author(s)

Xiuwen Zheng

### See Also

`snpgdsCreateGeno`, `snpgdsCreateGenoSet`, `snpgdsSNPList`, `snpgdsSNPListIntersect`

### Examples

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

    f <- snpgdsOpen(fn)
    samp_id <- read.gdsn(index.gdsn(f, "sample.id"))
    snp_id <- read.gdsn(index.gdsn(f, "snp.id"))
    geno <- read.gdsn(index.gdsn(f, "genotype"), start=c(1,1), count=c(-1, 3000))
    snpgdsClose(f)

    # split the GDS file with different samples
    snpgdsCreateGenoSet(fn, "t1.gds", sample.id=samp_id[1:10],
        snp.id=snp_id[1:3000])
    snpgdsCreateGenoSet(fn, "t2.gds", sample.id=samp_id[11:30],
        snp.id=snp_id[1:3000])

    # combine with different samples
    snpgdsCombineGeno(c("t1.gds", "t2.gds"), "test.gds", same.strand=TRUE)
    f <- snpgdsOpen("test.gds")
    g <- read.gdsn(index.gdsn(f, "genotype"))
    snpgdsClose(f)

    identical(geno[1:30, ], g)  # TRUE

    # split the GDS file with different SNPs
    snpgdsCreateGenoSet(fn, "t1.gds", snp.id=snp_id[1:100])
    snpgdsCreateGenoSet(fn, "t2.gds", snp.id=snp_id[101:300])

    # combine with different SNPs
    snpgdsCombineGeno(c("t1.gds", "t2.gds"), "test.gds")
    f <- snpgdsOpen("test.gds")
    g <- read.gdsn(index.gdsn(f, "genotype"))
    snpgdsClose(f)

    identical(geno[, 1:300], g)  # TRUE

    # delete the temporary files
    unlink(c("t1.gds", "t2.gds", "t3.gds", "t4.gds", "test.gds"), force=TRUE)

[Package SNPRelate version 1.14.0 Index]