Calculate the cell-feature distance matrix based on coembeddings.
pdistance(object, reduction = "fast", assay.name = "distce", eta = 1e-10)
Arguments
- object
a Seurat object.
- reduction
a opstional string, dimensional reduction name, `fast` by default.
- assay.name
a opstional string, specify the new generated assay name, `distce` by default.
- eta
an optional postive real, a quantity to avoid numerical errors. 1e-10 by default.
Details
This function calculate the distance matrix between cells/spots and features, and then put the distance matrix in a new generated assay. This
distance matrix will be used in the siganture gene identification.
Examples
data(pbmc3k_subset)
pbmc3k_subset <- NCFM(pbmc3k_subset)
#> 2025-03-15 08:43:56.204622 : ***** Finish CoFAST, 0.003 mins elapsed.
pbmc3k_subset <- pdistance(pbmc3k_subset, "ncfm")
#> Calculate co-embedding distance...