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