assignCellClusterNearestNode {phemd} | R Documentation

## Assign cells to a reference cell subtype

### Description

Assigns each cell in `cur_cells` to a cluster based on nearest cell in Monocle 2 tree

### Usage

    assignCellClusterNearestNode(
      cur_cells,
      ref_cells,
      ref_cell_labels,
      cell_model = c("monocle2", "seurat", "phate")
    )

### Arguments

`cur_cells` | Matrix of cells to be assigned to clusters (Dim: num_cells x num_markers)
`ref_cells` | Matrix of cells used to build reference Monocle 2 tree (Dim: num_monocle_cells x num_markers)
`ref_cell_labels` | Vector of length num_monocle_cells containing Monocle 2 cell branch assignments
`cell_model` | Either "monocle2", "seurat", or "phate" depending on method used to model cell state space

### Details

Private method (not exported in namespace). Uses RANN package for fast knn search

### Value

Vector of length num_cells representing cluster assignments for each cell in cur_cells

### Examples

    ## Not run:
    cur_cells_cluster_labels <- assignCellClusterNearestNode(cur_cells_expn_data,
    clustered_cells_expn_data, clustered_cells_cluster_labels, cell_model='monocle2')

    ## End(Not run)

[Package phemd version 1.10.0 Index]