controlForConfounders {OUTRIDER} | R Documentation |
This is the wrapper function for the autoencoder implementation. It can be used to call the standard R implementation or the experimental Python implementation.
controlForConfounders( ods, q, implementation = c("autoencoder", "pca"), BPPARAM = bpparam(), ... )
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
|
... |
Further arguments passed on to the specific implementation method. |
An ods object including the control factors
ods <- makeExampleOutriderDataSet() implementation <- 'autoencoder' ods <- estimateSizeFactors(ods) ods <- controlForConfounders(ods, implementation=implementation) plotCountCorHeatmap(ods, normalized=FALSE) plotCountCorHeatmap(ods, normalized=TRUE)