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

runScanpyFindHVG(
  inSCE,
  useAssay = "scanpyNormData",
  method = c("seurat", "cell_ranger", "seurat_v3"),
  altExpName = "featureSubset",
  altExp = FALSE,
  hvgNumber = 2000,
  minMean = 0.0125,
  maxMean = 3,
  minDisp = 0.5,
  maxDisp = Inf
)

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 log normalized data, except when flavor='seurat_v3', in which counts data is expected.
method: selected method to use for computation of highly variable genes. One of 'seurat', 'cell_ranger', or 'seurat_v3'. Default "seurat".
altExpName: Character. Name of the alternative experiment object to add if returnAsAltExp = TRUE. Default featureSubset.
altExp: Logical value indicating if the input object is an altExperiment. Default FALSE.
hvgNumber: numeric value of how many genes to select as highly variable. Default 2000
minMean: If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'. Default 0.0125
maxMean: If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'. Default 3
minDisp: If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'. Default 0.5
maxDisp: If n_top_genes unequals None, this and all other cutoffs for the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'. Default Inf

Value

Updated SingleCellExperiment object with highly variable genes computation stored getTopHVG, plotTopHVG

Examples

data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- runScanpyNormalizeData(sce, useAssay = "counts")
sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
g <- getTopHVG(sce, method = "seurat", hvgNumber = 500)
}