coFAST (version 0.2.0)

pdistance: Calculate the cell-feature distance matrix

Description

Calculate the cell-feature distance matrix based on coembeddings.

Usage

pdistance(object, reduction = "cofast", assay.name = "distce", eta = 1e-10)

Value

return a revised Seurat object with a assay slot `assay.name`.

Arguments

object

a Seurat object.

reduction

a optional string, dimensional reduction name, `cofast` by default.

assay.name

a optional string, specify the new generated assay name, `distce` by default.

eta

an optional positive 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)
pbmc3k_subset <- pdistance(pbmc3k_subset, "ncfm")