Compute a p-value for similarity using permutation — permute

Permute cluster labels to calculate empirical p-value

Usage

permute_similarity(
  expr_mat,
  ref_mat,
  cluster_ids,
  n_perm,
  per_cell = FALSE,
  compute_method,
  pseudobulk_method = "mean",
  rm0 = FALSE,
  ...
)

Arguments

expr_mat: single-cell expression matrix
ref_mat: reference expression matrix
cluster_ids: clustering info of single-cell data assume that genes have ALREADY BEEN filtered
n_perm: number of permutations
per_cell: run per cell?
compute_method: method(s) for computing similarity scores
pseudobulk_method: method used for summarizing clusters, options are mean (default), median, truncate (10% truncated mean), or trimean, max, min
rm0: consider 0 as missing data, recommended for per_cell
...: additional parameters

Value

matrix of numeric values