runSeuratTSNE: runSeuratTSNE Computes tSNE from the given sce object and...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

runSeuratTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object

Description

runSeuratTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object

Usage

runSeuratTSNE(
  inSCE,
  useReduction = c("pca", "ica"),
  reducedDimName = "seuratTSNE",
  dims = 10,
  perplexity = 30,
  externalReduction = NULL,
  seed = 1
)

Arguments

inSCE	(sce) object on which to compute the tSNE
useReduction	selected reduction algorithm to use for computing tSNE. One of "pca" or "ica". Default "pca".
reducedDimName	Name of new reducedDims object containing Seurat tSNE Default seuratTSNE.
dims	Number of reduction components to use for tSNE computation. Default 10.
perplexity	Adjust the perplexity tuneable parameter for the underlying tSNE call. Default 30.
externalReduction	Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.
seed	Random seed for reproducibility of results. Default 1.

Value

Updated sce object with tSNE computations stored

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.