run {spatialDE} | R Documentation |
Wraps the run
function from the
SpatialDE Python package.
run(x, coordinates, verbose = FALSE)
x |
|
coordinates |
|
verbose |
|
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
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 = 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)