GdsGenotypeReader {GWASTools} | R Documentation

## Class GdsGenotypeReader

### Description

The GdsGenotypeReader class is an extension of the GdsReader class specific to reading genotype data stored in GDS files. GDS files with both `snp x scan` and `scan x snp` dimensions are supported.

### Extends

`GdsReader`

### Constructor

  `GdsGenotypeReader(filename, genotypeDim)`:

  `filename` must be the path to a GDS file or a gds object. The GDS file must contain the following variables:

  - 'snp.id': a unique integer vector of snp ids

  - 'snp.chromosome': integer chromosome codes

  - 'snp.position': integer position values

  - 'sample.id': a unique integer vector of scan ids

  - 'genotype': a matrix of bytes with dimensions ('snp','sample'). The byte values must be the number of A alleles : 2=AA, 1=AB, 0=BB.

  The optional variable "snp.allele" stores the A and B alleles in a character vector with format "A/B".

  Default values for chromosome codes are 1-22=autosome, 23=X, 24=XY, 25=Y, 26=M. The defaults may be changed with the arguments `autosomeCode`, `XchromCode`, `XYchromCode`, `YchromCode`, and `MchromCode`.

  The constructor automatically detects whether the GDS file is in `snp x scan` or `scan x snp` order using the dimensions of `snp.id` and `sample.id`. In the case of GDS files with equal SNP and scan dimensions, `genotypeDim` is a required input to the function and can take values `"snp,scan"` or `"scan,snp"`.

  The `GdsGenotypeReader` constructor creates and returns a GdsGenotypeReader instance pointing to this file.

### Accessors

In the code snippets below, `object` is a GdsGenotypeReader object. See `GdsReader` for additional methods.

  `nsnp(object)`: The number of SNPs in the GDS file.

  `nscan(object)`: The number of scans in the GDS file.

  `getSnpID(object, index)`: A unique integer vector of snp IDs. The optional `index` is a logical or integer vector specifying elements to extract.

  `getChromosome(object, index, char=FALSE)`: A vector of chromosomes. The optional `index` is a logical or integer vector specifying elements to extract. If `char=FALSE` (default), returns an integer vector. If `char=TRUE`, returns a character vector with elements in (1:22,X,XY,Y,M,U). "U" stands for "Unknown" and is the value given to any chromosome code not falling in the other categories.

  `getPosition(object, index)`: An integer vector of base pair positions. The optional `index` is a logical or integer vector specifying elements to extract.

  `getAlleleA(object, index)`: A character vector of A alleles. The optional `index` is a logical or integer vector specifying elements to extract.

  `getAlleleB(object, index)`: A character vector of B alleles. The optional `index` is a logical or integer vector specifying elements to extract.

  `getScanID(object, index)`: A unique integer vector of scan IDs. The optional `index` is a logical or integer vector specifying elements to extract.

  `getGenotype(object, snp=c(1,-1), scan=c(1,-1), drop=TRUE, use.names=FALSE, order=c("file", "selection"), transpose=FALSE, ...)`: Extracts genotype values (number of A alleles). `snp` and `scan` indicate which elements to return along the snp and scan dimensions. They must be integer vectors of the form (start, count), where start is the index of the first data element to read and count is the number of elements to read. A value of '-1' for count indicates that the entire dimension should be read. If `drop=TRUE`, the result is coerced to the lowest possible dimension. If `use.names=TRUE`, names of the resulting vector or matrix are set to the SNP and scan IDs. Missing values are represented as `NA`. If `order=="file"`, genotypes are returned in the order they are stored in the file. If `order="selection"`, the order of SNPs and scans will match the index selection provided in `snp` and `scan` respectively. Genotypes are returned in SNP x scan order if transpose=FALSE, otherwise they are returned in scan x SNP order.

  `getGenotypeSelection(object, snp=NULL, scan=NULL, snpID=NULL, scanID=NULL, drop=TRUE, use.names=TRUE, transpose=FALSE, ...)`: Extracts genotype values (number of A alleles). `snp` and `scan` may be integer or logical vectors indicating which elements to return along the snp and scan dimensions. `snpID` and `scanID` allow section by values of snpID and scanID. Unlike `getGenotype`, the values requested need not be in contiguous blocks. Other arguments are identical to `getGenotype`.

  `getVariable(object, varname, index, drop=TRUE, ...)`: Extracts the contents of the variable `varname`. The optional `index` is a logical or integer vector (if `varname` is 1D) or list (if `varname` is 2D or higher) specifying elements to extract. If `drop=TRUE`, the result is coerced to the lowest possible dimension. Missing values are represented as `NA`. If the variable is not found, returns `NULL`.

  `XchromCode(object)`: Returns the integer code for the X chromosome.

  `XYchromCode(object)`: Returns the integer code for the pseudoautosomal region.

  `YchromCode(object)`: Returns the integer code for the Y chromosome.

  `MchromCode(object)`: Returns the integer code for mitochondrial SNPs.

### Author(s)

Stephanie Gogarten

### See Also

`GdsReader`, `GenotypeData`

### Examples

    file <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
    gds <- GdsGenotypeReader(file)

    # dimensions
    nsnp(gds)
    nscan(gds)

    # get snpID and chromosome
    snpID <- getSnpID(gds)
    chrom <- getChromosome(gds)

    # get positions only for chromosome 22
    pos22 <- getPosition(gds, index=(chrom == 22))

    # get all snps for first scan
    geno <- getGenotype(gds, snp=c(1,-1), scan=c(1,1))
    length(geno)

    # starting at snp 100, get 10 snps for the first 5 scans
    getGenotype(gds, snp=c(100,10), scan=c(1,5))

    # get snps 1-10, 25-30 for scans 3,5,7
    snp.index <- c(1:10, 25:30)
    scan.index <- c(3,5,7)
    getGenotypeSelection(gds, snp=snp.index, scan=scan.index)

    # illustrate drop argument
    getGenotypeSelection(gds, snp=5, scan=1:10, drop=TRUE, use.names=FALSE)
    getGenotypeSelection(gds, snp=5, scan=1:10, drop=FALSE, use.names=FALSE)

    # illustrate order="file" vs order="selection"
    snp.index <- c(9,3,5)
    scan.index <- c(3,2,1)
    getGenotypeSelection(gds, snp=snp.index, scan=scan.index, order="file")
    getGenotypeSelection(gds, snp=snp.index, scan=scan.index, order="selection")

    close(gds)

[Package GWASTools version 1.28.0 Index]