| snpgdsCreateGeno {SNPRelate} | R Documentation |
To create a GDS file of genotypes from a matrix.
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)
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
|
compress.geno |
the compression method for the variable
|
other.vars |
a list object storing other variables |
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.
None.
Xiuwen Zheng
snpgdsCreateGenoSet, snpgdsCombineGeno
# 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)