PseudobulkExpression {Seurat}

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.