get_similarity: Compute similarity of matrices

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

Compute similarity of matrices

Description

Compute similarity of matrices

Usage

get_similarity(
  expr_mat,
  ref_mat,
  cluster_ids,
  compute_method,
  pseudobulk_method = "mean",
  per_cell = FALSE,
  rm0 = FALSE,
  if_log = TRUE,
  low_threshold = 0,
  ...
)

Arguments

expr_mat	single-cell expression matrix
ref_mat	reference expression matrix
cluster_ids	vector of cluster ids for each 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
per_cell	run per cell?
rm0	consider 0 as missing data, recommended for per_cell
if_log	input data is natural log, averaging will be done on unlogged data
low_threshold	option to remove clusters with too few cells
...	additional parameters not used yet

Value

matrix of numeric values, clusters from expr_mat as row names, cell types from ref_mat as column names

NCBI-Hackathons/clustifyR documentation built on Aug. 31, 2024, 5:35 a.m.