Seurat (version 3.0.1)

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, 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).

use.scale

Use scaled values for gene expression

use.counts

Use count values for gene 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))

# }