RunTSNE {ILoReg} | R Documentation

## Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding (t-SNE)

### Description

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

### Usage

    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

    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)

[Package ILoReg version 1.2.0 Index]