model_search {spatialDE} | 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
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 )