R: Merge SNP datasets

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

Examples

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

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

snpgdsSummary("test.gds")

[Package SNPRelate version 1.10.2 Index]