controlForConfounders: Autoencoder function to correct for confounders.

Description Usage Arguments Value Examples

View source: R/controlForConfounders.R

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

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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

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

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

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

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