getTopHVG {singleCellTK} | R Documentation

## getTopHVG Extracts the top variable genes from an input singleCellExperiment object

### Description

getTopHVG Extracts the top variable genes from an input singleCellExperiment object

### Usage

    getTopHVG(inSCE, method, n = 2000)

### Arguments

`inSCE` | an input singleCellExperiment object
`method` | represents which method to use for variable gene extraction from either Seurat "vst", "mean.var.plot", "dispersion" or Scran "modelGeneVar"
`n` | number of top variable genes to extract

### Value

list of top variable gene names

### Author(s)

Irzam Sarfraz

### Examples

    data(sce_chcl, package = "scds")
    sce_chcl <- scranModelGeneVar(sce_chcl, "counts")
    # return top 10 variable genes
    topGenes <- getTopHVG(sce_chcl, "modelGeneVar", 10)

[Package singleCellTK version 2.2.0 Index]