retrieveRefClusters {phemd} | R Documentation

## Retrieve reference cell clusters

### Description

Takes initial Phemd struct and returns cell clusters as assigned by clustering algorithm (e.g. PHATE or Monocle2)

### Usage

    retrieveRefClusters(
      obj,
      cell_model = c("monocle2", "seurat", "phate"),
      expn_type = "reduced",
      ndim = 10
    )

### Arguments

`obj` | Phemd struct containing cell-state embedding object and underlying expression data
`cell_model` | String representing data model for cell-state space ("seurat", "monocle2", or "phate")
`expn_type` | String representing whether to return raw expression values or coordinates in dimensionality-reduced feature space
`ndim` | Number of dimensions in reduced dimensionality space (e.g. PHATE / CCA) to use (only relevant in reduced dimensionality space)

### Details

Private method (not exported in namespace)

### Value

List of data matrices; each list element is of size num_cells_in_cluster x num_markers and represents a distinct cell cluster

### Examples

    ## Not run:
    cluster_expression_data <- retrieveRefClusters(my_phemdObj)

    ## End(Not run)

[Package phemd version 1.6.0 Index]