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 1.0.0 Index]