spatialDE {spatialDE} | R Documentation

## Find spatially variable genes with SpatialDE

### Description

Identify genes that significantly depend on spatial coordinates with the SpatialDE Python package.

### Usage

    spatialDE(x, ...)

    ## S4 method for signature 'matrix'
    spatialDE(x, coordinates, verbose = FALSE)

    ## S4 method for signature 'SpatialExperiment'
    spatialDE(x, assay_type = "counts", verbose = FALSE)

### Arguments

`x` | A numeric `matrix` of counts where genes are rows and cells are columns. Alternatively, a SpatialExperiment object.
`...` | For the generic, arguments to pass to specific methods.
`coordinates` | A `data.frame` with sample coordinates. Each row is a sample, the columns with coordinates should be named 'x' and 'y'. For the SpatialExperiment method, coordinates are taken from `spatialCoords(x)`.
`verbose` | A `logical` controlling the display of a progress bar from the Python package.
`assay_type` | A `character` string specifying the assay from `x` to use as input. Defaults to `"counts"`.

### Value

A `data.frame` with DE results where each row is a gene and columns contain relevant statistics.

The most important columns are:

- `g`: the name of the gene

- `pval`: the p-value for spatial differential expression

- `qval`: the q-value, indicating significance after correcting for multiple testing

- `l`: A parameter indicating the distance scale a gene changes expression over

### Author(s)

Davide Corso, Milan Malfait, Lambda Moses

### References

Svensson, V., Teichmann, S. & Stegle, O. SpatialDE: identification of spatially variable genes. Nat Methods 15, 343–346 (2018). https://doi.org/10.1038/nmeth.4636

SpatialDE 1.1.3: the version of the Python package used under the hood.

### See Also

The individual steps performed by this function: `stabilize()`, `regress_out()` and `run()`.

For further analysis of the DE results: `model_search()` and `spatial_patterns()`.

### Examples

    ## Mock up a SpatialExperiment object wit 100 cells, 200 genes
    set.seed(42)
    spe <- mockSVG(size = 10, tot_genes = 200, de_genes = 20, return_SPE = TRUE)

    ## Run spatialDE
    de_results <- spatialDE(spe)

    head(de_results)

[Package spatialDE version 1.0.0 Index]