model_search {spatialDE} | R Documentation

## Compare model fits with different models

### Description

Classify DE genes to interpretable fitting classes.

### Usage

    model_search(x, coordinates, de_results, qval_thresh = 0.05, 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'.
`de_results` | `data.frame` resulting from `run()`.
`qval_thresh` | `numeric` scalar, specifying the q-value significance threshold to filter `de_results`. Only rows in `de_results` with `qval < qval_thresh` will be kept. To disable, set `qval_thresh = NULL`.
`verbose` | `logical` controlling the display of the progress bar.

### Value

`data.frame` of model_search results.

### 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 = 300, 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)

    ## Run model search
    ms_results <- model_search(
        x = regressed,
        coordinates = mock$coordinates,
        de_results = de_results,
        qval_thresh = NULL
    )

[Package spatialDE version 1.0.0 Index]