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'.

Description

Wrapper function to run one of the available dimensionality reduction algorithms integrated within the toolkit from 'scaterPCA', 'seuratPCA', 'seuratICA', 'rTSNE', 'seuratTSNE', 'uwotUMAP' and 'seuratUMAP'.

Usage

runDimensionalityReduction(
  inSCE,
  useAssay,
  reducedDimName,
  method = c("scaterPCA", "seuratPCA", "seuratICA", "rTSNE", "seuratTSNE", "uwotUMAP",
    "seuratUMAP"),
  nComponents = 10,
  ...
)

Arguments

inSCE

Input SingleCellExperiment object.

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 30) and 'nIterations' (default 1000). For 'seuratTSNE', must specify 'useReduction' (either 'pca' or 'ica') and 'perplexity' (default 30). For 'uwotUMAP', must specify 'nNeighbors' (default 30), 'nIterations' (default 200), 'minDist' (default 0.01) and 'alpha' (default 1). For 'seuratUMAP', must specify 'useReduction' (either 'pca' or 'ica'), 'minDist' (default 0.3), 'nNeighbors' (default 30) and 'spread' (default 1).

Value

A SingleCellExperiment object with PCA computation updated in reducedDim(inSCE, reducedDimName).

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runDimensionalityReduction(mouseBrainSubsetSCE,
                                                  "logcounts",
                                                  reducedDimName = "PCA")
[Package singleCellTK version 2.2.0 Index]