Normalize and run PCA with ChromSCape (LSI)

Source: R/processing.R

Runs ChromSCape LSI and removes the first component, often driven by total library size. See ChromSCape::preprocessing_filtering_and_reduction().

processing_ChromSCape(scExp, n_dims = 10, dim_red = "PCA")

Arguments

scExp

A Seurat object to preprocess with Seurat.
n_dims

An integer specifying the number of first dimensions to keep in the dimensionality reduction step.
dim_red

The name of the slot to save the dimensionality reduction at each step in the reducedDimNames(scExp).

Value

A SingleCellExperiment object with the dimensionality reduction filled