Create a SCtkExperiment
SCtkExperiment(..., pcaVariances = S4Vectors::DataFrame())SingleCellExperiment and SummarizedExperiment components
The percent variation contained in each PCA dimension
A SingleCellExperiment like object with an addition pcaVariances slot.
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