SCtkExperiment-class: A lightweight S4 extension to the SingleCellExperiment class...
In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

SCtkExperiment-class

R Documentation

A lightweight S4 extension to the SingleCellExperiment class to store additional information.

Description

A lightweight S4 extension to the SingleCellExperiment class to store additional information.

Arguments

value

The DataFrame of pcaVariances

Value

A SingleCellExperiment like object with an addition pcaVariances slot.

Slots

pcaVariances: The percent variation contained in each PCA dimension

Examples

data("mouseBrainSubsetSCE")
counts_mat <- assay(mouseBrainSubsetSCE, "counts")
sample_annot <- colData(mouseBrainSubsetSCE)
row_annot <- rowData(mouseBrainSubsetSCE)
newSCE <- SCtkExperiment(assays=list(counts=counts_mat),
                         colData=sample_annot,
                         rowData=row_annot)
newSCE <- getPCA(newSCE, useAssay = "counts")
#View the percent variation of the PCA
pcaVariances(newSCE)

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