GenotypeIterator-class {GWASTools} | R Documentation

## Class GenotypeIterator

### Description

Extends `GenotypeData` to provide iterators over SNPs.

### Details

Iterator classes allow for iterating over blocks of SNPs.

For `GenotypeBlockIterator`, each call to `iterateFilter` will select the next unit of `snpBlock` SNPs.

### Constructor

  `GenotypeBlockIterator(genoData, snpBlock=10000, snpInclude=NULL`: Returns a `GenotypeBlockIterator` object with the filter set to the first block.

  `genoData` is a `GenotypeData` object.

  `snpBlock` is an integer specifying the number of SNPs in an iteration block.

  `snpInclude` is a vector of snpIDs to include in the filter. If `NULL` (default), all SNPs are included.

### Accessors

  `iterateFilter(x)`: Advance the filter to the next block, range, or set of ranges. Returns `TRUE` while there are still variants left to be read, `FALSE` if the end of iteration is reached.

  `lastFilter(x)`, `lastFilter(x)<- value`: Get or set the last filter index from the previous call to `iterateFilter`.

  `snpFilter(x)`: Get the list of SNP indices.

  `currentFilter(x)`: Get the indices of SNPs selected in the current iteration.

  `resetIterator(x)`: Set the filter to the first block (the same SNPs that are selected when the iterator object is created).

  `getSnpID(object, ...)`: A unique integer vector of snp IDs.

  `getChromosome(object, ...)`: A vector of chromosomes.

  `getPosition(object, ...)`: An integer vector of base pair positions.

  `getAlleleA(object, ...)`: A character vector of A alleles.

  `getAlleleB(object, ...)`: A character vector of B alleles.

  `getGenotypeSelection(object, ...)`: Extracts genotype values (number of A alleles).

  `getSnpVariable(object, varname, ...)`: Returns the snp annotation variable `varname`.

Additional arguments for these accessors are passed to the corresponding methods for `GenotypeData` objects.

Other methods are inherited from `GenotypeData`.

### Author(s)

Stephanie Gogarten

### See Also

`GenotypeData`

### Examples

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

    iterator <- GenotypeBlockIterator(genoData, snpBlock=100)
    id <- getSnpID(iterator)
    length(id)
    head(id)
    geno <- getGenotypeSelection(iterator)
    dim(geno)
    geno <- getGenotypeSelection(iterator, scan=1:10)
    dim(geno)
    head(geno)

    iterateFilter(iterator)
    id <- getSnpID(iterator)
    length(id)
    head(id)
    geno <- getGenotypeSelection(iterator, scan=1:10)
    dim(geno)
    head(geno)

    close(iterator)

[Package GWASTools version 1.28.0 Index]