R/getTSNE.R
getTSNE.Rd
Run t-SNE dimensionality reduction method on a SingleCellExperiment Object
getTSNE( inSCE, useAssay = "logcounts", useAltExp = NULL, useReducedDim = NULL, reducedDimName = "TSNE", nIterations = 1000, perplexity = 30, run_pca = TRUE, ntop = NULL )
inSCE | Input SingleCellExperiment object. |
---|---|
useAssay | Assay to use for tSNE computation. If |
useAltExp | The subset to use for tSNE computation, usually for the
selected.variable features. Default |
useReducedDim | The low dimension representation to use for UMAP
computation. Default |
reducedDimName | a name to store the results of the dimension
reductions. Default |
nIterations | maximum iterations. Default |
perplexity | perplexity parameter. Default |
run_pca | run tSNE on PCA components? Default |
ntop | Number of top features to use as a further variable feature
selection. Default |
A SingleCellExperiment object with tSNE computation
updated in reducedDim(inSCE, reducedDimName)
.