processing_ChromSCape: Normalize and run PCA with ChromSCape (LSI)

In vallotlab/IDclust: Iterative Differential Clustering for single-cell

Normalize and run PCA with ChromSCape (LSI)

Description

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

Usage

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

Examples

data("scExp", package = "IDclust")
processing_ChromSCape(scExp)

vallotlab/IDclust documentation built on Feb. 16, 2023, 8:58 a.m.