retrieveRefClusters: Retrieve reference cell clusters

Description Usage Arguments Details Value Examples

View source: R/functions-core.R

Description

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

Usage

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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

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

## End(Not run)

phemd documentation built on April 29, 2020, 5:25 a.m.