run {spatialDE} | R Documentation

## Perform SpatialDE test

### Description

Wraps the `run` function from the SpatialDE Python package.

### Usage

    run(x, coordinates, verbose = FALSE)

### Arguments

`x` | `matrix`-like object of normalized counts. E.g. resulting from `regress_out()`.
`coordinates` | `data.frame` with sample coordinates. Each row is a sample, the columns with coordinates must be named 'x' and 'y'.
`verbose` | `logical` controlling the display of the progress bar.

### 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

### 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

### Examples

    set.seed(42)
    mock <- mockSVG(size = 10, tot_genes = 500, de_genes = 10)
    stabilized <- stabilize(mock$counts)
    sample_info <- mock$coordinates
    sample_info$total_counts <- colSums(mock$counts)
    regressed <- regress_out(counts = stabilized, sample_info = sample_info)

    ## Run SpatialDE
    de_results <- run(regressed, coordinates = mock$coordinates)

[Package spatialDE version 1.0.0 Index]