pdistance: Calculate the cell-feature distance matrix

In ProFAST: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

Calculate the cell-feature distance matrix

Description

Calculate the cell-feature distance matrix based on coembeddings.

Usage

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)
pbmc3k_subset <- pdistance(pbmc3k_subset, "ncfm")

ProFAST documentation built on May 29, 2024, 7:15 a.m.