Wrapper function for parameters for bootstrapped meta cell generation

This function generates parameters for the bootstrapped meta cell generation based on hdWGCNA, see Morabito, et al., Cell Rep. Methods, 2023.

Usage

params_sc_bt_metacells(
  max_shared = 15L,
  target_no_metacells = 1000L,
  max_iter = 5000L,
  knn = list()
)

Arguments

max_shared

Integer. Maximum number of allowed shared neighbours for the meta cell to be considered. Defaults to 15L.

target_no_metacells

Integer. Target number of meta-cells to generate. Defaults to 1000L.

max_iter

Integer. Maximum number of iterations for the algorithm. Defaults to 5000L.

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().

Value

A named list with the following elements:

• max_shared - Integer. Maximum number of allowed shared neighbours for the meta cell to be considered. Defaults to 15L.

• target_no_metacells - Integer. Target number of meta-cells to generate. Defaults to 1000L.

• max_iter - Integer. Maximum number of iterations for the algorithm. Defaults to 5000L.

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