R: Highly Variable Features

HVFInfo {SeuratObject} | R Documentation

## 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, ]

[Package SeuratObject version 4.0.3 Index]