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

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 Seurat
HVFInfo(object, selection.method = NULL, status = FALSE, assay = NULL, ...)

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

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

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

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

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

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

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

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

# S3 method for 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, ]
#>            mean    variance variance.standardized
#> MS4A1    0.3875   1.0251582             0.8983463
#> CD79B    0.6000   1.2810127             0.4731134
#> CD79A    0.7000   4.3645570             1.0862810
#> HLA-DRA 13.4250 725.4626582             0.9730883
#> TCL1A    0.3000   0.8708861             1.3558627

# Get the HVF info directly from an Assay object
HVFInfo(pbmc_small[["RNA"]], selection.method = 'vst')[1:5, ]
#>            mean    variance variance.standardized
#> MS4A1    0.3875   1.0251582             0.8983463
#> CD79B    0.6000   1.2810127             0.4731134
#> CD79A    0.7000   4.3645570             1.0862810
#> HLA-DRA 13.4250 725.4626582             0.9730883
#> TCL1A    0.3000   0.8708861             1.3558627