snpgdsCombineGeno: Merge SNP datasets

In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

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="ZIP_RA",
    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)

SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.