View source: R/compute_similarity.R
get_similarity | R Documentation |
Compute similarity of matrices
get_similarity(
expr_mat,
ref_mat,
cluster_ids,
compute_method,
pseudobulk_method = "mean",
per_cell = FALSE,
rm0 = FALSE,
if_log = TRUE,
low_threshold = 0,
...
)
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 |
matrix of numeric values, clusters from expr_mat as row names, cell types from ref_mat as column names
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