SpatialExperiment-assays {SpatialExperiment} | R Documentation

## 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)

[Package SpatialExperiment version 1.4.0 Index]