SNPRelate (version 1.6.4)

snpgdsGetGeno: To get a genotype matrix

Description

To get a genotype matrix from a specified GDS file

Usage

snpgdsGetGeno(gdsobj, sample.id=NULL, snp.id=NULL, snpfirstdim=NA, .snpread=NA, with.id=FALSE, verbose=TRUE)

Arguments

gdsobj

an object of class SNPGDSFileClass, a SNP GDS file; or characters to specify the file name of SNP GDS

sample.id

a vector of sample id specifying selected samples; if NULL, all samples are used

snp.id

a vector of snp id specifying selected SNPs; if NULL, all SNPs are used

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); FALSE for snp-major mode; if NA, determine automatically

.snpread

internal use

with.id

if TRUE, return sample.id and snp.id

verbose

if TRUE, show information

Value

The function returns an integer matrix with values 0, 1, 2 or NA representing the number of reference allele when with.id=FALSE; or list(genotype, sample.id, snp.id) when with.id=TRUE. The orders of sample and SNP IDs in the genotype matrix are actually consistent with sample.id and snp.id in the GDS file, which may not be as the same as the arguments sampel.id and snp.id specified by users.

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

set.seed(1000)
snpset <- sample(read.gdsn(index.gdsn(genofile, "snp.id")), 1000)

mat1 <- snpgdsGetGeno(genofile, snp.id=snpset, snpfirstdim=TRUE)
dim(mat1)
# 1000  279
table(c(mat1), exclude=NULL)

mat2 <- snpgdsGetGeno(genofile, snp.id=snpset, snpfirstdim=FALSE)
dim(mat2)
# 279 1000
table(c(mat2), exclude=NULL)

identical(t(mat1), mat2)
# TRUE

# close the file
snpgdsClose(genofile)