getPCA: Get and plot PCA components for a SCtkE object

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

Get and plot PCA components for a SCtkE object

Description

Selects the 500 most variable genes in the SCE, performs PCA based on them and stores the values in the reducedDims slot of the SCE object.

Usage

getPCA(inSCE, useAssay = "logcounts", reducedDimName = "PCA")

Arguments

inSCE	Input SCtkExperiment object. Required
useAssay	Indicate which assay to use for PCA. Default is "counts"
reducedDimName	Store the PCA data with this name. The default is PCA. The toolkit will store data with the pattern <ASSAY>_<ALGORITHM>.

Value

A SCtkE object with the specified reducedDim and pcaVariances updated

Examples

data("mouseBrainSubsetSCE")
#add a CPM assay
assay(mouseBrainSubsetSCE, "cpm") <- apply(assay(mouseBrainSubsetSCE,
                                                 "counts"),
                                           2, function(x) {
                                             x / (sum(x) / 1000000)
                                           })
mouseBrainSubsetSCE <- getPCA(mouseBrainSubsetSCE,
                              useAssay = "cpm",
                              reducedDimName = "PCA_cpm")
reducedDims(mouseBrainSubsetSCE)

mmkhan19/singleCellTK documentation built on March 22, 2022, 7:43 a.m.