AverageExpression: Averaged feature expression by identity class

In ibseq/scs-analysis: Tools for Single Cell Genomics

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,
  slot = "data",
  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	Categories for grouping (e.g, ident, replicate, celltype); 'ident' by default
add.ident	(Deprecated) Place an additional label on each cell prior to pseudobulking (very useful if you want to observe cluster pseudobulk values, separated by replicate, for example)
slot	Slot(s) to use; if multiple slots are given, assumed to follow the order of 'assays' (if specified) or object's assays
verbose	Print messages and show progress bar
...	Arguments to be passed to methods such as CreateSeuratObject

Details

If slot 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 slot is set to either 'counts' or 'scale.data', no exponentiation is performed prior to averaging If return.seurat = TRUE and slot is not 'scale.data', averaged values are placed in the 'counts' slot of the returned object and the log of averaged values are placed in the 'data' slot. ScaleData is then run on the default assay before returning the object. If return.seurat = TRUE and slot is 'scale.data', the 'counts' slot is left empty, the 'data' slot is filled with NA, and 'scale.data' is set to the aggregated values.

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))

ibseq/scs-analysis documentation built on Feb. 27, 2021, 12:35 a.m.