Run t-SNE dimensionality reduction method on the assay data.

getTSNE(inSCE, useAssay = "logcounts", reducedDimName = "TSNE",
  n_iterations = 1000, perplexity = NULL)

Arguments

inSCE

Input SCtkExperiment object. Required

useAssay

Indicate which assay to use. The default is "logcounts".

reducedDimName

a name to store the results of the dimension reductions

n_iterations

maximum iterations. Default is 1000

perplexity

perplexity parameter. Default is 5

Value

A SCtkE object with the specified reducedDim and pcaVariances updated

Examples

data("mouseBrainSubsetSCE") #add a CPM assay assay(mouseBrainSubsetSCE, "cpm") <- apply( assay(mouseBrainSubsetSCE, "counts"), 2, function(x) { x / (sum(x) / 1000000) }) mouseBrainSubsetSCE <- getTSNE(mouseBrainSubsetSCE, useAssay = "cpm", reducedDimName = "TSNE_cpm") reducedDims(mouseBrainSubsetSCE)
#> List of length 5 #> names(5): PCA_counts PCA_logcounts TSNE_counts TSNE_logcounts TSNE_cpm