controlForConfounders {OUTRIDER} | R Documentation

## Autoencoder function to correct for confounders.

### Description

This is the wrapper function for the autoencoder implementation. It can be used to call the standard R implementation or the experimental Python implementation.

### Usage

    controlForConfounders(
      ods,
      q,
      implementation = c("autoencoder", "pca"),
      BPPARAM = bpparam(),
      ...
    )

### Arguments

`ods` | An OutriderDataSet object
`q` | The encoding dimensions
`implementation` | "autoencoder", the default, will use the autoencoder implementation. Also 'pca' and 'peer' can be used to control for confounding effects
`BPPARAM` | A `BiocParallelParam` instance to be used for parallel computing.
`...` | Further arguments passed on to the specific implementation method.

### Value

An ods object including the control factors

### Examples

    ods <- makeExampleOutriderDataSet()
    implementation <- 'autoencoder'

    ods <- estimateSizeFactors(ods)
    ods <- controlForConfounders(ods, implementation=implementation)

    plotCountCorHeatmap(ods, normalized=FALSE)
    plotCountCorHeatmap(ods, normalized=TRUE)

[Package OUTRIDER version 1.10.0 Index]