seuratPCA {singleCellTK} | R Documentation

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

### Description

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

### Usage

    seuratPCA(
      inSCE,
      useAssay = "seuratScaledData",
      reducedDimName = "seuratPCA",
      nPCs = 20,
      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`.
`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")
    ## 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)

[Package singleCellTK version 2.2.0 Index]