SNPRelate (version 1.6.4)

snpgdsCreateGeno: Create a SNP genotype dataset from a matrix

Description

To create a GDS file of genotypes from a matrix.

Usage

snpgdsCreateGeno(gds.fn, genmat, sample.id=NULL, snp.id=NULL, snp.rs.id=NULL, snp.chromosome=NULL, snp.position=NULL, snp.allele=NULL, snpfirstdim=TRUE, compress.annotation="ZIP_RA.max", compress.geno="", other.vars=NULL)

Arguments

gds.fn

the file name of gds

genmat

a matrix of genotypes

sample.id

the sample ids, which should be unique

snp.id

the SNP ids, which should be unique

snp.rs.id

the rs ids for SNPs, which can be not unique

snp.chromosome

the chromosome indices

snp.position

the SNP positions in basepair

snp.allele

the reference/non-reference alleles

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

Value

None.

Details

There are possible values stored in the variable genmat: 0, 1, 2 and other values. ``0'' indicates two B alleles, ``1'' indicates one A allele and one B allele, ``2'' indicates two A alleles, and other values indicate a missing genotype.

If snpfirstdim is TRUE, then genmat should be ``# of SNPs X # of samples''; if snpfirstdim is FALSE, then genmat should be ``# of samples X # of SNPs''.

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

See Also

snpgdsCreateGenoSet, snpgdsCombineGeno

Examples

# load data
data(hapmap_geno)

# create a gds file
with(hapmap_geno, snpgdsCreateGeno("test.gds", genmat=genotype,
    sample.id=sample.id, snp.id=snp.id, snp.chromosome=snp.chromosome,
    snp.position=snp.position, snp.allele=snp.allele, snpfirstdim=TRUE))

# open the gds file
genofile <- snpgdsOpen("test.gds")

RV <- snpgdsPCA(genofile)
plot(RV$eigenvect[,2], RV$eigenvect[,1], xlab="PC 2", ylab="PC 1")

# close the file
snpgdsClose(genofile)