SpatialExperiment-assays {SpatialExperiment} | R Documentation |
The SpatialExperiment
class provides methods for getting or
setting named assays
. For example, molecules(spe)
will
get or set an assay
named molecules
from object spe
,
equivalent to assay(spe, i = "molecules")
. This provides a convenient
interface for users and encourages standardization of assay names across
packages.
In the following code, spe
is a SpatialExperiment
object, value
is a BumpyMatrix
-like object with the same
dimensions as spe
, and ...
are further arguments passed to
assay
(for the getter) or assay<-
(for the
setter).
molecules(x, ...)
, molecules(x, ...) <- value
:Get or set an assay named molecules
, which is usually assumed to be a
BumpyMatrix
-formatted object containing spatial coordinates (and any
other information) of the individual molecules per gene per cell.
Dario Righelli
example(SpatialExperiment) molecules(spe_mol)