average_clusters {clustifyr} | R Documentation |
Average expression values per cluster
average_clusters( mat, metadata, cluster_col = "cluster", if_log = TRUE, cell_col = NULL, low_threshold = 0, method = "mean", output_log = TRUE, subclusterpower = 0, cut_n = NULL )
mat |
expression matrix |
metadata |
data.frame or vector containing cluster assignments per cell. Order must match column order in supplied matrix. If a data.frame provide the cluster_col parameters. |
cluster_col |
column in metadata with cluster number |
if_log |
input data is natural log, averaging will be done on unlogged data |
cell_col |
if provided, will reorder matrix first |
low_threshold |
option to remove clusters with too few cells |
method |
whether to take mean (default), median, 10% truncated mean, or trimean |
output_log |
whether to report log results |
subclusterpower |
whether to get multiple averages per original cluster |
cut_n |
set on a limit of genes as expressed, lower ranked genes are set to 0, considered unexpressed |
average expression matrix, with genes for row names, and clusters for column names
mat <- average_clusters( mat = pbmc_matrix_small, metadata = pbmc_meta, cluster_col = "classified", if_log = FALSE ) mat[1:3, 1:3]