AggregateExpression: Aggregated feature expression by identity class

In satijalab/seurat: Tools for Single Cell Genomics

Aggregated feature expression by identity class

Description

Returns summed counts ("pseudobulk") for each identity class.

Usage

AggregateExpression(
  object,
  assays = NULL,
  features = NULL,
  return.seurat = FALSE,
  group.by = "ident",
  add.ident = NULL,
  normalization.method = "LogNormalize",
  scale.factor = 10000,
  margin = 1,
  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
normalization.method	Method for normalization, see NormalizeData
scale.factor	Scale factor for normalization, see NormalizeData
margin	Margin to perform CLR normalization, see NormalizeData
verbose	Print messages and show progress bar
...	Arguments to be passed to methods such as CreateSeuratObject

Details

If return.seurat = TRUE, aggregated values are placed in the 'counts' layer of the returned object. The data is then normalized by running NormalizeData on the aggregated counts. ScaleData is then run on the default assay before returning the object.

Value

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

Examples

## Not run: 
data("pbmc_small")
head(AggregateExpression(object = pbmc_small)$RNA)
head(AggregateExpression(object = pbmc_small, group.by = c('ident', 'groups'))$RNA)

## End(Not run)

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