runSeuratPCA Computes PCA on the input sce object and stores the calculated principal components within the sce object

runSeuratPCA(
  inSCE,
  useAssay = "seuratScaledData",
  reducedDimName = "seuratPCA",
  nPCs = 20,
  features = NULL,
  seed = NULL,
  verbose = TRUE
)

Arguments

inSCE: (sce) object on which to compute PCA
useAssay: Assay containing scaled counts to use in PCA.
reducedDimName: Name of new reducedDims object containing Seurat PCA. Default seuratPCA.
nPCs: numeric value of how many components to compute. Default 20.
features: Specify the feature names or rownames which should be used for computation of PCA. Default is NULL which will use the previously stored variable features.
seed: Random seed for reproducibility of results. Default NULL will use global seed in use by the R environment.
verbose: Logical value indicating if informative messages should be displayed. Default is TRUE.

Value

Updated SingleCellExperiment object which now contains the computed principal components

Examples

data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratPCA(sce, useAssay = "counts")
}