AverageExpression: Averaged gene expression by identity class

In mayer-lab/SeuratForMayer2018: Seurat : R Toolkit for Single Cell Genomics

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

Details

Output is in log-space, but averaging is done in non-log space.

Value

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

mayer-lab/SeuratForMayer2018 documentation built on May 25, 2019, 9:34 p.m.