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Generate CAGRA GPU kNN data for single cells (deprecated)

generate_cagra_knn_sc.Rd

[Deprecated]

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

Usage

generate_cagra_knn_sc(
  object,
  embd_to_use = "pca",
  cells_to_use = NULL,
  no_embd_to_use = NULL,
  modality = c("rna", "adt"),
  cagra_params = params_nn_gpu(),
  extract_knn = TRUE,
  seed = 42L,
  .verbose = TRUE
)

Arguments

object

SingleCells (or SingleCellsMultiModal) class.

embd_to_use

String. The embedding to use.

cells_to_use

Optional string vector. Cell names to include.

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.

seed

Integer. For reproducibility.

.verbose

Boolean or integer. Controls verbosity.

Value

Initialised sc_knn with the kNN data.