Pseudobulk Expression — PseudobulkExpression • Seurat

Normalize the count data present in a given assay.

Returns a representative expression value for each identity class

PseudobulkExpression(object, ...)

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

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

# S3 method for 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 use; 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.