Materialize a Bioconductor assay container from some facile object.

Most often, this will be from some facile_frame to create a Bioconductor assay container object, but this function can be overloaded for other purposes.

biocbox(x, ...)

# S3 method for facile_frame
biocbox(
  x,
  class = NULL,
  assay_name = NULL,
  features = NULL,
  sample_covariates = NULL,
  feature_covariates = NULL,
  normalized = FALSE,
  with_fds = FALSE,
  custom_key = Sys.getenv("USER"),
  ...
)

Arguments

x	A facile object
sample_covariates	If NULL (default), all sample covariates will be included over samples in x. If a data.frame, we will treat the extra columns as custom covariates, and include them in the outgoing box, along with the internal ones.

Details

The FacileAnalysis package, for example, uses this function to materialize bioconductor objects of different flavors from different analysis results, ie. a DGEList, or perhaps a limma fit object, etc.

facile_frame

We can materialize a Bioconductor data container for a given assay over a set of samples.

There is a default bioc class provided for different assay types, however the class type can be overrided by the class parameter. This function simply puts the assay data requested into the container. There is no sepcial functionality that happens downstream of that (for instance, DGEList lib.size calculated from the data that made its way into the DGEList)