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 1.20.1 Index]