GetCellGeneDistance: Distance Calculation

Description Usage Arguments Value

View source: R/cell.R

Description

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

Usage

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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 Nov. 12, 2019, 1:36 a.m.