AverageExpression: Averaged feature expression by identity class

In satijalab/seurat: Tools for Single Cell Genomics

Averaged feature expression by identity class

Description

Returns averaged expression values for each identity class.

Usage

AverageExpression(
  object,
  assays = NULL,
  features = NULL,
  return.seurat = FALSE,
  group.by = "ident",
  add.ident = NULL,
  layer = "data",
  slot = deprecated(),
  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
group.by	Category (or vector of categories) for grouping (e.g, ident, replicate, celltype); 'ident' by default To use multiple categories, specify a vector, such as c('ident', 'replicate', 'celltype')
add.ident	(Deprecated). Place an additional label on each cell prior to pseudobulking
layer	Layer(s) to use; if multiple layers are given, assumed to follow the order of 'assays' (if specified) or object's assays
slot	(Deprecated). Slots(s) to use
verbose	Print messages and show progress bar
...	Arguments to be passed to methods such as CreateSeuratObject

Details

If layer is set to 'data', this function assumes that the data has been log normalized and therefore feature values are exponentiated prior to averaging so that averaging is done in non-log space. Otherwise, if layer is set to either 'counts' or 'scale.data', no exponentiation is performed prior to averaging. If return.seurat = TRUE and layer is not 'scale.data', averaged values are placed in the 'counts' layer of the returned object and 'log1p' is run on the averaged counts and placed in the 'data' layer ScaleData is then run on the default assay before returning the object. If return.seurat = TRUE and layer is 'scale.data', the 'counts' layer contains average counts and 'scale.data' is set to the averaged values of 'scale.data'.

Value

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

Examples

data("pbmc_small")
head(AverageExpression(object = pbmc_small)$RNA)
head(AverageExpression(object = pbmc_small, group.by = c('ident', 'groups'))$RNA)

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.