SeuratObject: VariableFeatures – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

VariableFeatures

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

HVFInfo(object, selection.method, status = FALSE, ...)

VariableFeatures(object, selection.method = NULL, ...)

VariableFeatures(object, ...) <- value

SVFInfo(object, selection.method, status, ...)

SpatiallyVariableFeatures(object, selection.method, ...)

## S3 method for class 'Seurat'
HVFInfo(object, selection.method = NULL, status = FALSE, assay = NULL, ...)

## S3 method for class 'Seurat'
VariableFeatures(object, selection.method = NULL, assay = NULL, ...)

## S3 replacement method for class 'Seurat'
VariableFeatures(object, assay = NULL, ...) <- value

## S3 method for class 'Seurat'
SVFInfo(
  object,
  selection.method = c("markvariogram", "moransi"),
  status = FALSE,
  assay = NULL,
  ...
)

## S3 method for class 'Seurat'
SpatiallyVariableFeatures(
  object,
  selection.method = "markvariogram",
  assay = NULL,
  decreasing = TRUE,
  ...
)

## S3 method for class 'Assay'
HVFInfo(object, selection.method, status = FALSE, ...)

## S3 method for class 'Assay'
SpatiallyVariableFeatures(
  object,
  selection.method = "markvariogram",
  decreasing = TRUE,
  ...
)

## S3 method for class 'Assay'
SVFInfo(
  object,
  selection.method = c("markvariogram", "moransi"),
  status = FALSE,
  ...
)

## S3 method for class 'Assay'
VariableFeatures(object, selection.method = NULL, ...)

## S3 replacement method for class 'Assay'
VariableFeatures(object, ...) <- value

Arguments

`object`	An object
`selection.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
`...`	Arguments passed to other methods
`value`	A character vector of variable features
`assay`	Name of assay to pull highly variable feature information for
`decreasing`	Return features in decreasing order (most spatially variable first).

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

Examples

# Get the HVF info from a specific Assay in a Seurat object
HVFInfo(object = pbmc_small, assay = "RNA")[1:5, ]

# Get the HVF info directly from an Assay object
HVFInfo(pbmc_small[["RNA"]], selection.method = 'vst')[1:5, ]

SeuratObject

Data Structures for Single Cell Data

v4.0.1

GPL-3

Authors

Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>), Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>), Jeff Farrell [ctb], Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Patrick Roelli [ctb], Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)

Initial release

2021-05-07