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

runSeuratFindHVG(
  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")
if (FALSE) {
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
}