permute_similarity: Compute a p-value for similarity using permutation

In NCBI-Hackathons/RClusterCT: Classifier for Single-cell RNA-seq Using Cell Clusters

Compute a p-value for similarity using permutation

Description

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

NCBI-Hackathons/RClusterCT documentation built on June 12, 2025, 9:37 p.m.