biocbox | R Documentation |
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 class '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"),
...
)
x |
A facile object |
sample_covariates |
If |
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.
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)
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