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    0.2680210
#> PC2    0.1551645
#> PC3    0.0740499
#> PC4    0.0655109
#> PC5    0.0505161
#> ...          ...
#> PC26 6.72633e-03
#> PC27 4.90804e-03
#> PC28 4.74709e-03
#> PC29 4.41731e-03
#> PC30 5.28578e-32