Seurat (version 3.1.4)

AverageExpression: Averaged feature expression by identity class

Description

Returns expression for an 'average' single cell in each identity class

Usage

AverageExpression(
  object,
  assays = NULL,
  features = NULL,
  return.seurat = FALSE,
  add.ident = NULL,
  slot = "data",
  use.scale = FALSE,
  use.counts = FALSE,
  verbose = TRUE,
  ...
)

Arguments

object

Seurat object

assays

Which assays to use. Default is all assays

features

Features to analyze. Default is all features in the assay

return.seurat

Whether to return the data as a Seurat object. Default is FALSE

add.ident

Place an additional label on each cell prior to averaging (very useful if you want to observe cluster averages, separated by replicate, for example)

slot

Slot to use; will be overriden by use.scale and use.counts

use.scale

Use scaled values for feature expression

use.counts

Use count values for feature expression

verbose

Print messages and show progress bar

...

Arguments to be passed to methods such as CreateSeuratObject

Value

Returns a matrix with genes as rows, identity classes as columns. If return.seurat is TRUE, returns an object of class Seurat.

Details

Output is in log-space when return.seurat = TRUE, otherwise it's in non-log space. Averaging is done in non-log space.

Examples

# NOT RUN {
head(AverageExpression(object = pbmc_small))

# }