PseudobulkExpression: Pseudobulk Expression

In satijalab/seurat: Tools for Single Cell Genomics

Pseudobulk Expression

Description

Normalize the count data present in a given assay.

Returns a representative expression value for each identity class

Usage

PseudobulkExpression(object, ...)

## S3 method for class 'Assay'
PseudobulkExpression(
  object,
  assay,
  category.matrix,
  features = NULL,
  layer = "data",
  slot = deprecated(),
  verbose = TRUE,
  ...
)

## S3 method for class 'StdAssay'
PseudobulkExpression(
  object,
  assay,
  category.matrix,
  features = NULL,
  layer = "data",
  slot = deprecated(),
  verbose = TRUE,
  ...
)

## S3 method for class 'Seurat'
PseudobulkExpression(
  object,
  assays = NULL,
  features = NULL,
  return.seurat = FALSE,
  group.by = "ident",
  add.ident = NULL,
  layer = "data",
  slot = deprecated(),
  method = "average",
  normalization.method = "LogNormalize",
  scale.factor = 10000,
  margin = 1,
  verbose = TRUE,
  ...
)

Arguments

object	Seurat object
...	Arguments to be passed to methods such as CreateSeuratObject
assay	The name of the passed assay - used primarily for warning/error messages
category.matrix	A matrix defining groupings for pseudobulk expression calculations; each column represents an identity class, and each row a sample
features	Features to analyze. Default is all features in the assay
layer	Layer(s) to user; if multiple are given, assumed to follow the order of 'assays' (if specified) or object's assays
slot	(Deprecated) See layer
verbose	Print messages and show progress bar
assays	Which assays to use. Default is all assays
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) See group.by
method	The method used for calculating pseudobulk expression; one of: "average" or "aggregate"
normalization.method	Method for normalization, see NormalizeData
scale.factor	Scale factor for normalization, see NormalizeData
margin	Margin to perform CLR normalization, see NormalizeData

Value

Returns object after normalization

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

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