SpatialExperiment-assays: Methods for named assays

In drighelli/VisiumExperiment: S4 Class for Spatially Resolved -omics Data

Methods for named assays

Description

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.

Available methods

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.

Author(s)

Dario Righelli

See Also

assay and assay<-

Examples

example(SpatialExperiment)
molecules(spe_mol)

drighelli/VisiumExperiment documentation built on June 30, 2024, 10:55 a.m.