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Find neighbours via CAGRA GPU-acceleration for single cells (deprecated)

find_neighbours_cagra_sc.Rd

[Deprecated]

CAGRA now sits behind find_neighbours_gpu_sc() as knn_method = "nndescent".

Usage

find_neighbours_cagra_sc(
  object,
  embd_to_use = "pca",
  no_embd_to_use = NULL,
  modality = c("rna", "adt"),
  cagra_params = params_nn_gpu(),
  extract_knn = FALSE,
  snn_params = params_sc_neighbours(),
  seed = 42L,
  .verbose = TRUE
)

Arguments

object

SingleCells (or SingleCellsMultiModal) class.

embd_to_use

String. The embedding to use.

no_embd_to_use

Optional integer. Number of embedding dimensions.

modality

String. One of c("rna", "adt").

cagra_params

List. Output of the deprecated params_sc_cagra(), or params_nn_gpu().

extract_knn

Logical. Skip the beam search.

snn_params

List. Output of bixverse::params_sc_neighbours().

seed

Integer. For reproducibility.

.verbose

Boolean. Controls verbosity.

Value

The object with added kNN matrix and sNN graph.