Wrapper function for the fastMNN parameters

Wrapper function for the fastMNN parameters

Usage

params_sc_fastmnn(
  ndist = 3,
  cos_norm = TRUE,
  no_pcs = 30L,
  sparse_svd = TRUE,
  knn = list(k = 20L),
  pca = params_sc_pca()
)

Arguments

ndist

Numeric. Number of median distances for the tricube kernel bandwidth. Defaults to 3.0.

cos_norm

Boolean. Apply cosine normalisation before computing distances. Defaults to TRUE.

no_pcs

Integer. Number of PCs to use for MNN calculations. Defaults to 30L.

sparse_svd

Boolean. Shall the sparse SVD be used. Defaults to TRUE.

knn

List. Optional overrides for kNN parameters. See params_knn_defaults() for available parameters: k, knn_method, ann_dist, search_budget, n_trees, delta, diversify_prob, ef_budget, extract_knn, m, ef_construction, ef_search, n_list and n_probe. See params_knn_defaults() for the available elements. Defaults to list(k = 20L).

pca

List. Parameters to feed through to the optional recalculation of the PCA, see params_sc_pca(). See params_sc_pca() for the available elements. Defaults to params_sc_pca().

Value

A named list with the following elements:

• ndist - Numeric. Number of median distances for the tricube kernel bandwidth. Defaults to 3.0.

• cos_norm - Boolean. Apply cosine normalisation before computing distances. Defaults to TRUE.

• no_pcs - Integer. Number of PCs to use for MNN calculations. Defaults to 30L.

• sparse_svd - Boolean. Shall the sparse SVD be used. Defaults to TRUE.

• The elements of params_knn_defaults(), overridden by knn, spliced in at this position.

• The elements of params_sc_pca(), overridden by pca, spliced in at this position.