set_cds_nn_index: Set a nearest neighor index in the cell_data_set.

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Set a nearest neighor index in the cell_data_set.

Description

Store the given nearest neighbor index in the cell_data_set. The reduction_method parameter tells set_cds_nn_index where in the cell_data_set to store the index.

Usage

set_cds_nn_index(
  cds,
  reduction_method = c("UMAP", "PCA", "LSI", "Aligned", "tSNE"),
  nn_index,
  verbose = FALSE
)

Arguments

cds	a cell_data_set in which to store the nearest neighbor index.
reduction_method	a string giving the reduced dimension matrix used to make the nn_index nearest neighbor index, and determines where the index is stored in the cell_data_set.
nn_index	a nearest neighbor index to store in cds.
verbose	a boolean indicating whether to emit verbose output.

Value

a cell_data_set with the stored index.

cole-trapnell-lab/monocle3 documentation built on April 7, 2024, 9:24 p.m.