Get Genotype Matrix

Extract a genotype matrix from an object that carries genotype data. For an LdData, returns the underlying genotype matrix via its handle (or NULL if no handle is available). For a QtlDataset, returns the genotype matrix for a selected set of traits or region (see method documentation for the per-class selection arguments).

Usage

getGenotypes(x, ...)

# S4 method for class 'LdData'
getGenotypes(x, ...)

# S4 method for class 'QtlDataset'
getGenotypes(
  x,
  traitId = NULL,
  region = NULL,
  cisWindow = NULL,
  samples = NULL,
  ...
)

Arguments

x

The object to extract from.

...

Class-specific selection arguments (e.g., traitId, region, cisWindow for QtlDataset).

Value

A numeric matrix, a list of matrices, or NULL.