seuratPCA {singleCellTK} | R Documentation |
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, verbose = TRUE )
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 |
nPCs |
numeric value of how many components to compute. Default
|
verbose |
Logical value indicating if informative messages should
be displayed. Default is |
Updated SingleCellExperiment
object which now contains the
computed principal components
data(scExample, package = "singleCellTK") ## Not run: sce <- seuratNormalizeData(sce, useAssay = "counts") sce <- seuratFindHVG(sce, useAssay = "counts") sce <- seuratScaleData(sce, useAssay = "counts") sce <- seuratPCA(sce, useAssay = "counts") ## End(Not run)