modelSearch: Classify Spatially Variable Genes to interpretable fitting...

In sales-lab/spatialDE: R wrapper for SpatialDE

Classify Spatially Variable Genes to interpretable fitting classes

Description

Compare model fits with different models, using the SpatialDE Python package.

Usage

modelSearch(x, de_results, ...)

## S4 method for signature 'matrix'
modelSearch(x, de_results, coordinates, qval_thresh = 0.05, verbose = FALSE)

## S4 method for signature 'SpatialExperiment'
modelSearch(
  x,
  de_results,
  assay_type = "counts",
  qval_thresh = 0.05,
  verbose = FALSE
)

Arguments

x	A numeric matrix of counts where genes are rows and cells are columns. Alternatively, a SpatialExperiment object.
de_results	data.frame resulting from run() or spatialDE().
...	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).
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	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

data.frame of model_search results.

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 model_search().

Examples

## Mock up a SpatialExperiment object wit 400 cells and 3 genes
set.seed(42)
spe <- mockSVG(size = 20, tot_genes = 3, de_genes = 1, return_SPE = TRUE)

## Run spatialDE with S4 integration
de_results <- spatialDE(spe)

## Run model search
model_search <- modelSearch(spe, de_results = de_results,
    qval_thresh = NULL, verbose = FALSE
)

sales-lab/spatialDE documentation built on Feb. 12, 2024, 2:47 p.m.