R: To get a genotype matrix

snpgdsGetGeno {SNPRelate}

R Documentation

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.

Author(s)

Xiuwen Zheng

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)

[Package SNPRelate version 1.10.2 Index]