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, sum

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

Examples

mat <- average_clusters(data.frame(
  z = c(1, 2, 3, 4, 5, 6),
  y = c(1, 2, 3, 4, 5, 6),
  x = c(1, 2, 3, 4, 5, 6)
), metadata = c(1, 1, 2), method = "sum")

[Package colorrepel version 0.4.1 Index]