get_similarity: Compute similarity of matrices

View source: R/compute_similarity.R

get_similarityR Documentation

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/RClusterCT documentation built on July 10, 2022, 6:18 a.m.