OUTRIDER {OUTRIDER} | R Documentation

## OUTRIDER - Finding expression outlier events

### Description

The OUTRIDER function runs the default OUTRIDER pipeline combinig the fit, the computation of Z scores and P-values. All computed values are returned as an OutriderDataSet object.

To have more control over each analysis step, one can call each function separately.

1. `estimateSizeFactors` to calculate the sizeFactors

2. `controlForConfounders` to control for confounding effects

3. `fit` to fit the negative binomial model (only needed if the autoencoder is not used)

4. `computePvalues` to calculate the nominal and adjusted P-values

5. `computeZscores` to calculate the Z scores

### Usage

    OUTRIDER(
      ods,
      q,
      controlData = TRUE,
      implementation = "autoencoder",
      BPPARAM = bpparam(),
      ...
    )

### Arguments

`ods` | An OutriderDataSet object
`q` | The encoding dimensions
`controlData` | If TRUE, the default, the raw counts are controled for confounders by the autoencoder
`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 `controlForConfounders`

### Value

OutriderDataSet with all the computed values. The values are stored as assays and can be accessed by: `assay(ods, 'value')`. To get a full list of calculated values run: `assayNames(ods)`

### Examples

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

    ods <- OUTRIDER(ods, implementation=implementation)

    pValue(ods)[1:10,1:10]
    res <- results(ods, all=TRUE)
    res

    plotAberrantPerSample(ods)
    plotVolcano(ods, 1)

[Package OUTRIDER version 1.10.0 Index]