Calculate the cell-feature distance matrix

Source: R/CoFAST.R

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)
#> 2024-03-17 18:26:44 : ***** Finish CoFAST, 0.007 mins elapsed.
pbmc3k_subset <- pdistance(pbmc3k_subset, "ncfm")
#> Calculate co-embedding distance...