snpgdsCombineGeno: Merge SNP datasets

In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

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.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.

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")

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Create test.gds with 558 samples and 9087 SNPs
	Open the gds file /usr/local/lib/R/site-library/SNPRelate/extdata/hapmap_geno.gds.
		0 strands of SNP loci need to be switched.
	Open the gds file /usr/local/lib/R/site-library/SNPRelate/extdata/hapmap_geno.gds.
		0 strands of SNP loci need to be switched.
Warning messages:
1: In snpgdsCombineGeno(gds.fn = gds.fn, out.fn = out.fn, sample.id = sample.id,  :
  1 SNPs allele mis-matched and removed.
2: In snpgdsCombineGeno(gds.fn = gds.fn, out.fn = out.fn, sample.id = sample.id,  :
  1 SNPs allele mis-matched and removed.
3: In snpgdsCombineGeno(c(fn, fn), "test.gds") :
  Has specified the value of `name.prefix' to make sample id unique.
The file name: /work/tmp/test.gds 
The total number of samples: 558 
The total number of SNPs: 9087 
SNP genotypes are stored in individual-major mode (SNP X Sample).

SNPRelate documentation built on May 2, 2019, 4:56 p.m.