GetCellGeneDistance {CelliD} | R Documentation

## Distance Calculation

### Description

Small intermediate function for euclidean distance calculation between MCA feature coordinates and cell coordinates. Due to MCA pseudo barycentric relationship, the closer a gene g is to a cell c, the more specific to such a cell it can be considered.

### 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 embedding and loading for distance calculation.
`features` | Character vector of feature names to subset feature coordinates. If not specified will take all features available from specified reduction Loading.
`cells` | Character vector of cell names to subset cell coordinates. If not specified will take all cells available from specified reduction Embedding.

### Value

Distance Matrix with genes at row and cells at column

[Package CelliD version 1.2.1 Index]