View source: R/classify_SVGs.R
model_search | R Documentation |
Classify DE genes to interpretable fitting classes.
model_search(x, coordinates, de_results, qval_thresh = 0.05, verbose = FALSE)
x |
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coordinates |
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de_results |
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qval_thresh |
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verbose |
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data.frame
of model_search results.
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
## Mock up a SpatialExperiment object wit 400 cells and 3 genes
set.seed(42)
mock <- mockSVG(size = 20, tot_genes = 3, de_genes = 1)
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
)
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