runZINBWaVE {singleCellTK} | R Documentation

## Apply ZINBWaVE Batch effect correction method to SingleCellExperiment object

### Description

A general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of scRNAseq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates.

### Usage

    runZINBWaVE(
      inSCE,
      useAssay = "counts",
      batch = "batch",
      nHVG = 1000L,
      nComponents = 50L,
      epsilon = 1000,
      nIter = 10L,
      reducedDimName = "zinbwave"
    )

### Arguments

`inSCE` | SingleCellExperiment inherited object. Required.
`useAssay` | A single character indicating the name of the assay requiring batch correction. Note that ZINBWaVE works for counts (integer) input rather than logcounts that other methods prefer. Default `"counts"`.
`batch` | A single character indicating a field in `colData` that annotates the batches. Default `"batch"`.
`nHVG` | An integer. Number of highly variable genes to use when fitting the model. Default `1000L`.
`nComponents` | An integer. The number of principle components or dimensionality to generate in the resulting matrix. Default `50L`.
`epsilon` | An integer. Algorithmic parameter. Empirically, a high epsilon is often required to obtained a good low-level representation. Default `1000L`.
`nIter` | An integer, The max number of iterations to perform. Default `10L`.
`reducedDimName` | A single character. The name for the corrected low-dimensional representation. Will be saved to `reducedDim(inSCE)`. Default `"zinbwave"`.

### Value

The input SingleCellExperiment object with `reducedDim(inSCE, reducedDimName)` updated.

### References

Pollen, Alex A et al., 2014

### Examples

    data('sceBatches', package = 'singleCellTK')
    ## Not run:
        sceCorr <- runZINBWaVE(sceBatches, nIter = 5)

    ## End(Not run)

[Package singleCellTK version 2.0.0 Index]