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]