retrieveRefClusters {phemd} | R Documentation

## Retrieve reference cell clusters

### Description

Takes initial Phemd struct and returns cell clusters as assigned by clustering algorithm (i.e. Monocle 2)

### Usage

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

### Arguments

`obj` | Phemd struct containing Monocle2 object and underlying expression data
`cell_model` | String representing data model for cell state space (Seurat or Monocle 2)
`expn_type` | String representing whether to return raw expression values or coordinates in dimensionality-reduced, aligned feature space (only relevant for Seurat data models)
`ndim` | Number of dimensions (e.g. CCA) to use (only relevant for Seurat data models)

### 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 1.0.1 Index]