R/seuratFunctions.R
seuratPCA.Rd
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, 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
|
features | Specify the feature names or rownames which should be used
for computation of PCA. Default is |
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") if (FALSE) { sce <- seuratNormalizeData(sce, useAssay = "counts") sce <- seuratFindHVG(sce, useAssay = "counts") sce <- seuratScaleData(sce, useAssay = "counts") sce <- seuratPCA(sce, useAssay = "counts") }