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