Prepare class for contrastive PCA — contrastive_pca_processing • bixverse

This function will prepare the BulkCoExp for subsequent usage of the contrastive PCA functions. This is based on the work of Abid, et al.

Usage

contrastive_pca_processing(
  object,
  background_matrix,
  scale = FALSE,
  .verbose = TRUE
)

Arguments

object: The underlying class, see BulkCoExp().
background_matrix: Numeric matrix. The background matrix you wish to remove. You should apply any data transformation to this matrix, too!
scale: Boolean. Shall the data be scaled. Defaults to FALSE.
.verbose: Boolean. Controls verbosity of the function.

Value

BulkCoExp with the needed data for contrastive PCA in the properties of the class.

References

Abid, et al., Nature Communications, 2018