OUTRIDER: OUTRIDER - Finding expression outlier events

Description Usage Arguments Value Examples

View source: R/OUTRIDER.R

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

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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

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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)

gagneurlab/OUTRIDER documentation built on Oct. 24, 2020, 6:49 p.m.