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Parameters for the CellPhoneDB analysis

params_sc_cellphonedb.Rd

Defaults match CellPhoneDB v5: 1000 permutations and a 10% expression threshold.

Usage

params_sc_cellphonedb(
  n_perm = 1000L,
  threshold = 0.1,
  seed = 42L,
  perm_batch = NULL
)

Arguments

n_perm

Integer. Number of cluster label permutations for the p-values. Defaults to 1000L.

threshold

Numeric. Both partners need a fraction of expressing cells strictly above this value in their cluster. Defaults to 0.1.

seed

Integer. Seed for the permutations. Defaults to 42L.

perm_batch

Integer or NULL. Permutations that share one pass over the gene data. NULL uses the Rust default (16). Defaults to NULL.

Value

A named list with the following elements:

  • n_perm - Integer. Number of cluster label permutations for the p-values. Defaults to 1000L.

  • threshold - Numeric. Both partners need a fraction of expressing cells strictly above this value in their cluster. Defaults to 0.1.

  • seed - Integer. Seed for the permutations. Defaults to 42L.

  • perm_batch - Integer or NULL. Permutations that share one pass over the gene data. NULL uses the Rust default (16). Defaults to NULL.