RunUMAP: Uniform Manifold Approximation and Projection (UMAP)

In elolab/ILoReg: ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

Uniform Manifold Approximation and Projection (UMAP)

Description

Run nonlinear dimensionality reduction using UMAP with the PCA-transformed consensus matrix as input.

Usage

RunUMAP.SingleCellExperiment(object)

## S4 method for signature 'SingleCellExperiment'
RunUMAP(object)

Arguments

object

of SingleCellExperiment class

Value

object of SingleCellExperiment class

Examples

library(SingleCellExperiment)
sce <- SingleCellExperiment(assays = list(logcounts = pbmc3k_500))
sce <- PrepareILoReg(sce)
## These settings are just to accelerate the example, use the defaults.
sce <- RunParallelICP(sce,L=2,threads=1,C=0.1,k=5,r=1)
sce <- RunPCA(sce,p=5)
sce <- RunUMAP(sce)

elolab/ILoReg documentation built on March 28, 2022, 1:17 a.m.