Get PCA reduction from an expression matrix

This function calculates the PCA embedding of an expression matrix.

Usage

pca_reduction(expr_matrix, npcs = 30, approx = FALSE, ...)

Arguments

expr_matrix

The gene by cell expression matrix to be used. It is expected that the matrix is already normalized and scaled.

npcs

The number of principal components to be used. Defaults to 30.

approx

Logical indicating if deterministic PCA (with prcomp) or approximate PCA (with irlba) should be used. Defaults to FALSE.

...

Aditional parameters passed to the PCA function.

Value

A gene by npcs matrix containing the PCA embedding.

Note

The PCA is applied in this context to the genes, not to the cells.