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, reducedDimName = "seuratPCA", nPCs = 20)

### 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`.

### 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 2.0.0 Index]