SeuratObject (version 5.0.2)

VariableFeatures-StdAssay: Highly Variable Features

Description

Get and set variable feature information for an Assay object. HVFInfo and VariableFeatures utilize generally variable features, while SVFInfo and SpatiallyVariableFeatures are restricted to spatially variable features

Usage

# S3 method for StdAssay
HVFInfo(object, method = NULL, status = FALSE, layer = NULL, strip = TRUE, ...)
# S3 method for StdAssay
VariableFeatures(
  object,
  method = NULL,
  layer = NA,
  simplify = TRUE,
  nfeatures = Inf,
  selection.method = deprecated(),
  ...
)
# S3 method for StdAssay
VariableFeatures(object, method = "custom", layer = NULL, ...) <- value

Value

HVFInfo: A data frame with feature means, dispersion, and scaled dispersion

VariableFeatures: a vector of the variable features

SVFInfo: a data frame with the spatially variable features

SpatiallyVariableFeatures: a character vector of the spatially variable features

Arguments

object

An object

method

Which method to pull. For HVFInfo and VariableFeatures, choose one from one of the following:

• “vst”

• “sctransform” or “sct”

• “mean.var.plot”, “dispersion”, “mvp”, or “disp”

For SVFInfo and SpatiallyVariableFeatures, choose from:

• “markvariogram”

• “moransi”

status

Add variable status to the resulting data frame

layer

Layer to pull variable features for

strip

Remove method/layer identifiers from highly variable data frame

...

Arguments passed to other methods

simplify

When pulling for multiple layers, combine into a single vector and select a common set of variable features for all layers

nfeatures

Maximum number of features to select when simplifying

selection.method

lifecycle::badge("deprecated")

value

A character vector of variable features