MatrixGenotypeReader {GWASTools} | R Documentation

## Class MatrixGenotypeReader

### Description

The MatrixGenotypeReader class stores a matrix of genotypes as well as SNP and scan IDs, chromosome, and position.

### Constructor

  `MatrixGenotypeReader(genotype=genotype, snpID=snpID, chromosome=chromosome, position=position, scanID=scanID)`:

  `genotype` must be a matrix with dimensions ('snp','scan') containing the number of A alleles : 2=AA, 1=AB, 0=BB.

  `snp` must be a unique integer vector of SNP ids.

  `chromosome` must be an integer vector of chromosomes. 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`.

  `position` must be an integer vector of base positions

  `scanID` must be a unique integer vector of scan ids .

The `MatrixGenotypeReader` constructor creates and returns a MatrixGenotypeReader instance.

### Accessors

In the code snippets below, `object` is a MatrixGenotypeReader object.

  `nsnp(object)`: The number of SNPs.

  `nscan(object)`: The number of scans.

  `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.

  `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)`: 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`.

  `getGenotypeSelection(object, snp=NULL, scan=NULL, snpID=NULL, scanID=NULL, drop=TRUE, use.names=TRUE)`: 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. If `order=="file"`, genotypes are returned in the order they are stored in the object. If `order="selection"`, the order of SNPs and scans will match the index selection provided in `snp` and `scan` respectively. Other arguments are identical to `getGenotype`.

  `autosomeCode(object)`: Returns the integer codes for the autosomes.

  `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

`NcdfGenotypeReader`, `GenotypeData`

### Examples

    snpID <- 1:100
    chrom <- rep(1:20, each=5)
    pos <- 1001:1100
    scanID <- 1:20
    geno <- matrix(sample(c(0,1,2,NA), 2000, replace=TRUE), nrow=100, ncol=20)

    mgr <- MatrixGenotypeReader(genotype=geno, snpID=snpID,
      chromosome=chrom, position=pos, scanID=scanID)

    # dimensions
    nsnp(mgr)
    nscan(mgr)

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

    # get positions only for chromosome 10
    pos10 <- getPosition(mgr, index=(chrom == 10))

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

    # starting at snp 50, get 10 snps for the first 5 scans
    geno <- getGenotype(mgr, snp=c(50,10), scan=c(1,5))

[Package GWASTools version 1.32.0 Index]