runDimensionalityReduction {singleCellTK} | R Documentation |
Wrapper function to run one of the available dimensionality reduction algorithms integrated within the toolkit from 'scaterPCA', 'seuratPCA', 'seuratICA', 'rTSNE', 'seuratTSNE', 'uwotUMAP' and 'seuratUMAP'.
runDimensionalityReduction( inSCE, useAssay, reducedDimName, method = c("scaterPCA", "seuratPCA", "seuratICA", "rTSNE", "seuratTSNE", "uwotUMAP", "seuratUMAP"), nComponents = 10, ... )
inSCE |
Input |
useAssay |
Specify the name of the assay that should be used. |
reducedDimName |
Specify the name of the output reducedDim. |
method |
Specify a method from 'scaterPCA', 'seuratPCA', 'seuratICA', 'rTSNE', 'seuratTSNE', 'uwotUMAP' and 'seuratUMAP'. |
nComponents |
Specify the number of dimensions to compute with the selected method. Only applicable with 'scaterPCA', 'seuratPCA', 'seuratICA', 'seuratTSNE' and 'seuratUMAP' methods. |
... |
Additional parameters for the selected method.
For 'rTSNE', must specify 'perplexity' (default |
A SingleCellExperiment object with PCA computation
updated in reducedDim(inSCE, reducedDimName)
.
data("mouseBrainSubsetSCE", package = "singleCellTK") mouseBrainSubsetSCE <- runDimensionalityReduction(mouseBrainSubsetSCE, "logcounts", reducedDimName = "PCA")