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Calculate PCA on the expression.

calculate_pca_bulk_dge.Rd

Calculates the principal component on top of the filtered count matrix and adds the information of the first 10 principal components to the outputs.

Usage

calculate_pca_bulk_dge(
  object,
  scale_genes = FALSE,
  pcs = 10L,
  no_hvg_genes = 2500L
)

Arguments

object

The underlying class, see BulkDge().

scale_genes

Boolean. Shall the log(cpm) counts be scaled prior the PCA calculation. Defaults to FALSE.

pcs

Integer. Number of PCs to return and add to the outputs slot.

no_hvg_genes

Integer. Number of highly variable genes to include. Defaults to 2500.

Value

Returns the class with additional data added to the outputs.