retrieveRefClusters {phemd} | R Documentation |
Takes initial Phemd struct and returns cell clusters as assigned by clustering algorithm (i.e. Monocle 2)
retrieveRefClusters(obj, cell_model = c("monocle2", "seurat"), expn_type = "aligned", ndim = 10)
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) |
Private method (not exported in namespace)
List of data matrices; each list element is of size num_cells_in_cluster x num_markers and represents a distinct cell cluster
## Not run: cluster_expression_data <- retrieveRefClusters(my_phemdObj) ## End(Not run)