seuratPCA: seuratPCA Computes PCA on the input sce object and stores the...

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.