retrieveRefClusters: Retrieve reference cell clusters

In phemd: Phenotypic EMD for comparison of single-cell samples

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)

phemd documentation built on Nov. 8, 2020, 8:15 p.m.