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)
#> DataFrame with 30 rows and 1 column #> percentVar #> <numeric> #> PC1 0.268020978932062 #> PC2 0.15516450073815 #> PC3 0.0740498509896174 #> PC4 0.0655109274462671 #> PC5 0.0505161060145296 #> ... ... #> PC26 0.00672632989322181 #> PC27 0.00490804359387214 #> PC28 0.0047470942300841 #> PC29 0.00441731197240141 #> PC30 5.2857818014642e-32