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

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

seuratPCA(
  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 <- seuratNormalizeData(sce, useAssay = "counts")
sce <- seuratFindHVG(sce, useAssay = "counts")
sce <- seuratScaleData(sce, useAssay = "counts")
sce <- seuratPCA(sce, useAssay = "counts")
}