Distances.pre_embedding: Calculation of pre-embedding distances

In JSB-UCLA/scDED: Single-cell Dubious Embedding Detector

Calculation of pre-embedding distances

Description

This function calculates the distances between cells in the pre-embedding space for the original and permuted data

Usage

Distances.pre_embedding(pbmc, pbmc_permuted, K, pre_embedding = 'pca')

Arguments

pbmc	The original Seurat object
pbmc_permuted	The permuted Seurat object, i.e. the output of Permuted.
K	The number of PCs to use
pre_embedding	Which embedding set to use for distance calculation, default = 'pca'. If the user would like to use an alternate method, like ICA, they should perform that method for the original and permuted data, then specify the slot name here

Value

Returns a list with two distance matrices, (1) 'pre_embedding_distances': a matrix showing the distances between cells in the original pre-embedding space (2) 'pre_embedding_distances_permuted': a matrix showing the distances between cells in the permuted pre-embedding space

JSB-UCLA/scDED documentation built on Feb. 8, 2025, 11:12 a.m.