Seurat (version 2.3.4)

AverageExpression: Averaged gene expression by identity class

Description

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

Usage

AverageExpression(object, genes.use = NULL, return.seurat = FALSE,
  add.ident = NULL, use.scale = FALSE, use.raw = FALSE,
  show.progress = TRUE, ...)

Arguments

object

Seurat object

genes.use

Genes to analyze. Default is all genes.

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.raw

Use raw values for gene expression

show.progress

Show progress bar (default is T)

...

Arguments to be passed to methods such as Seurat

Value

Returns a matrix with genes as rows, identity classes as columns.

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))

# }