SCtkExperiment-class: A lightweight S4 extension to the SingleCellExperiment class...

Description Arguments Value Slots Examples

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

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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)

singleCellTK documentation built on June 26, 2018, 10 a.m.