Wrapper function for the GPU BBKNN parameters

GPU counterpart to bixverse::params_sc_bbknn(). Same BBKNN knobs, but the kNN block is the GPU one, see params_knn_gpu_defaults().

Usage

params_sc_bbknn_gpu(
  neighbours_within_batch = 3L,
  set_op_mix_ratio = 1,
  local_connectivity = 1,
  trim = NULL,
  knn = list()
)

Arguments

neighbours_within_batch

Integer. Number of neighbours to consider per batch. Defaults to 3L.

set_op_mix_ratio

Numeric. Mixing ratio between union (1.0) and intersection (0.0). Defaults to 1.0.

local_connectivity

Numeric. UMAP connectivity computation parameter, how many nearest neighbours of each cell are assumed to be fully connected. Defaults to 1.0.

trim

Optional integer. Trim the neighbours of each cell to these many top connectivities. May help with population independence and improve the tidiness of clustering. If NULL, it defaults to 10 * neighbours_within_batch.

knn

List. Optional overrides for the kNN block. Validated against params_knn_gpu_defaults() minus k and extract_knn. Unknown keys are an error, not a silent pass-through.

Value

A flat named list with all GPU BBKNN parameters.

Details

Two keys of the GPU kNN block do nothing here and are rejected rather than silently ignored. k is set by neighbours_within_batch, and extract_knn only applies to a self-query, whereas BBKNN builds one index per batch and queries each with every cell.

References

Polański, et al., Bioinformatics, 2020