seuratFindHVG {singleCellTK} | R Documentation

## seuratFindHVG Find highly variable genes and store in the input sce object

### Description

seuratFindHVG Find highly variable genes and store in the input sce object

### Usage

    seuratFindHVG(
      inSCE,
      useAssay = "counts",
      hvgMethod = "vst",
      hvgNumber = 2000,
      altExp = FALSE,
      verbose = TRUE
    )

### Arguments

`inSCE` | (sce) object to compute highly variable genes from and to store back to it
`useAssay` | Specify the name of the assay to use for computation of variable genes. It is recommended to use a raw counts assay with the 'vst' method and normalized assay with all other methods. Default is `"counts"`.
`hvgMethod` | selected method to use for computation of highly variable genes. One of 'vst', 'dispersion', or 'mean.var.plot'. Default method is 'vst' which uses the raw counts. All other methods use normalized counts.
`hvgNumber` | numeric value of how many genes to select as highly variable. Default `2000`
`altExp` | Logical value indicating if the input object is an altExperiment. Default `FALSE`.
`verbose` | Logical value indicating if informative messages should be displayed. Default is `TRUE`.

### Value

Updated `SingleCellExperiment` object with highly variable genes computation stored

### Examples

    data(scExample, package = "singleCellTK")
    ## Not run:
    sce <- seuratNormalizeData(sce, useAssay = "counts")
    sce <- seuratFindHVG(sce, useAssay = "counts")

    ## End(Not run)

[Package singleCellTK version 2.2.0 Index]