mash Prior-Covariance Settings

How the prior covariance matrices (the Ulist mash consumes) are obtained: supplied outright, or built from components and refined by an engine. Exactly the arguments mashPriorCovariances takes for that job, so the bundle travels there whole.

Supplying priorCovariances short-circuits the rest: the components are not built and the engine does not run.

Usage

MashPriorParam(
  priorCovariances = NULL,
  components = c("canonical", "pca", "flash", "flashNonneg"),
  engine = c("covEd", "covUdr", "none"),
  nPcs = NULL
)

Arguments

priorCovariances

Optional named list of square covariance matrices, or a MashPrior. NULL (default) builds them.

components

Which prior-covariance components to build: any of "canonical", "pca", "flash", "flashNonneg", or a MashComponentParam record to configure them. Ignored when priorCovariances is supplied.

engine

How the data-driven components are refined: "covEd" (default), "covUdr" or "none", or the matching constructor — CovEdOptions / CovUdrOptions — to configure it at the same time. Ignored when priorCovariances is supplied.

nPcs

Optional integer; principal components seeded into mashr::cov_pca(). Defaults to ncol of the data. Read only when components includes "pca".

Value

A MashPriorParam object, a MethodParam.

Examples

MashPriorParam(components = c("canonical", "pca"), nPcs = 3)
#> <MashPriorParam>
#>   components               canonical, pca
#>   engine                   <covEd: algorithm>
#>   nPcs                     3
#>   unset: priorCovariances