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]