Select variable genes from one dataset with Seurat VST method

Seurat FindVariableFeatures VST method. This allows the selection of a fixed number of variable features, but only applies to one dataset. No normalization is needed in advance.

Usage

selectGenesVST(
  object,
  useDataset,
  n = 2000,
  loessSpan = 0.3,
  clipMax = "auto",
  useShared = TRUE,
  verbose = getOption("ligerVerbose", TRUE)
)

Arguments

object

A liger object.

useDataset

The names, a numeric or logical index of the dataset to be considered for selection.

n

Number of variable features needed. Default 2000.

loessSpan

Loess span parameter used when fitting the variance-mean relationship. Default 0.3.

clipMax

After standardization values larger than clipMax will be set to clipMax. Default "auto" sets this value to the square root of the number of cells.

useShared

Logical. Whether to only select from genes shared by all dataset. Default TRUE.

verbose

Logical. Whether to show information of the progress. Default getOption("ligerVerbose") or TRUE if users have not set.

References

Seurat::FindVariableFeatures.default(selection.method = "vst")

Examples

pbmc <- selectGenesVST(pbmc, "ctrl", n = 50)
#> ℹ Selecting top 50 HVGs with VST method for dataset: "ctrl"
#> ℹ ... Totally 249 shared genes to be selected from.