Skip to contents

Generate a new SingleCellNearestNeighbour from data

generate_sc_knn.Rd

Generate a new SingleCellNearestNeighbour from data

Usage

generate_sc_knn(
  data,
  neighbours_params = params_sc_neighbours(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

data

Numerical matrix. Samplex x features. The embedding matrix from which to generate the kNN data.

neighbours_params

List. Output of params_sc_neighbours(). A list with the following items:

  • full_snn - Boolean. Shall the full shared nearest neighbour graph be generated that generates edges between all cells instead of between only neighbours. (Not used in this function.)

  • pruning - Numeric. Weights below this threshold will be set to 0 in the generation of the sNN graph. (Not used in this function.)

  • snn_similarity - String. One of c("rank", "jaccard"). Defines how the weight from the SNN graph is calculated. For details, please see params_sc_neighbours(). (Not used in this function.)

  • knn - List of kNN parameters. See params_knn_defaults() for available parameters and their defaults.

seed

Integer. Random seed for reproducibility.

.verbose

Boolean. Controls verbosity.

Value

The SingleCellNearestNeighbour for downstream usage.