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

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") if (FALSE) { sce <- seuratNormalizeData(sce, useAssay = "counts") sce <- seuratFindHVG(sce, useAssay = "counts") }