getTopHVG: getTopHVG Extracts the top variable genes from an input...

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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 <- scran_modelGeneVar(sce_chcl, "counts")
# return top 10 variable genes
topGenes <- getTopHVG(sce_chcl, "modelGeneVar", 10)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.