average_clusters {colorrepel} | R Documentation |
Average expression values per cluster
Description
Average expression values per cluster
Usage
average_clusters(
mat,
metadata,
cluster_col = "cluster",
if_log = TRUE,
cell_col = NULL,
low_threshold = 0,
method = "mean",
output_log = TRUE,
cut_n = NULL
)
Arguments
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, max, min |
output_log |
whether to report log results |
cut_n |
set on a limit of genes as expressed, lower ranked genes are set to 0, considered unexpressed |
Value
average or other desired calculation by group/cluster matrix
[Package colorrepel version 0.1.0 Index]