runPca: runPca()

In navinlabcode/copykit: CopyKit

runPca()

Description

Creates a pca embedding using the package uwot from the segment ratios values

Usage

runPca(scCNA, assay = "logr", name = "PCA", scale = FALSE, ...)

Arguments

scCNA	The CopyKit object.
assay	String with the name of the assay to pull data from to make the embedding.
name	String specifying the name to be used to store the result in the reducedDims of the output.
scale	A logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place.
...	Additional parameters passed to prcomp.

Value

A reduced dimension representation with pca in the slot reducedDim from scCNA object. Access reduced dimensions slot with: reducedDim(scCNA, 'PCA', withDimnames = FALSE)

Author(s)

Darlan Conterno Minussi

Examples

set.seed(1000)
copykit_obj <- copykit_example_filtered()[,sample(100)]
copykit_obj <- runPca(copykit_obj)

navinlabcode/copykit documentation built on Sept. 22, 2023, 9:16 a.m.