GetCellGeneDistance: Distance Calculation

In cbl-imagine/CellID: Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis

Description

Small intermediate function for euclidean distance calculation between MCA feture coordinates and cell coordinates.

Usage

GetCellGeneDistance(X, reduction, dims, features, cells)

## S3 method for class 'Seurat'
GetCellGeneDistance(X, reduction = "mca", dims,
  features = NULL, cells = NULL)

## S3 method for class 'SingleCellExperiment'
GetCellGeneDistance(X, reduction = "MCA",
  dims, features = NULL, cells = NULL)

Arguments

X	Seurat or SingleCell Experiment Object
reduction	Which dimensionality reduction to use, must be based on MCA.
dims	A vector of integers indicating which dimensions to use with reduction embeddings and loadings for distance calculation.
features	Character vector of feature names to subset feature coordinates. If not specified will take all features available from specified reduction Loadings.
cells	Character vector of cell names to subset cell coordinates. If not specified will take all cells available from specified reduction Embeddings.

Value

Distance Matrix with genes at row and cellls at column

cbl-imagine/CellID documentation built on July 22, 2020, 7:18 p.m.