update a SingleCellExperiment with PCA (via irlba) reductions of embeddings produced with PyTorch-BigGraph

pca_CG(trout, sce, ncomp = 3, ...)

Arguments

trout: output of `BiocPBG::train_eval`
sce: SingleCellExperiment instance derived from or consistent with the one from which `trout` was produced
ncomp: numeric(1) passed as `n` to `irlba::prcomp_irlba`
...: named arguments other than `n` to be passed to irlba

Value

The `sce` is updated to include a `reducedDim` component named `PCA` based on the cell embedding, and the rowData component is updated to include the PCA applied to gene embedding

Examples

data(nn50)
data(t3k)
twp = pca_CG(nn50, t3k)
pairs(reducedDim(twp, "PCA"), pch=19, col=factor(twp$celltype3))