RunTSNE: Barnes-Hut implementation of t-Distributed Stochastic...

Description Usage Arguments Value Examples

Description

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

Usage

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RunTSNE.SingleCellExperiment(object, perplexity)

## S4 method for signature 'SingleCellExperiment'
RunTSNE(object, perplexity = 30)

Arguments

object

of SingleCellExperiment class

perplexity

perplexity of t-SNE

Value

object of SingleCellExperiment class

Examples

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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 <- RunTSNE(sce)

ILoReg documentation built on Nov. 8, 2020, 8:20 p.m.