Extract phenotype data from an object that carries it.
For a QtlDataset, the user can optionally select specific
contexts, traits, or a region (see method documentation for the
per-class selection arguments).
Usage
getPhenotypes(x, ...)
# S4 method for class 'QtlDataset'
getPhenotypes(
x,
contexts,
traitId = NULL,
region = NULL,
naAction = c("keep", "drop", "impute"),
outlierAction = c("keep", "drop"),
outlierPvalThreshold = 0.001,
...
)
Arguments
- x
The object to extract from.
- ...
Class-specific selection arguments (e.g., contexts,
traitId, region).
Value
A named list of phenotype matrices or
SummarizedExperiment objects.