run.tSNE: Wraper for running Rtsne

In Japrin/sscClust: simpler single cell RNAseq data clustering

Wraper for running Rtsne

Description

Wraper for running Rtsne

Usage

run.tSNE(
  idata,
  tSNE.usePCA = T,
  tSNE.perplexity = 30,
  method = "Rtsne",
  n.cores = NULL,
  out.prefix = NULL,
  ...
)

Arguments

idata	matrix; expression data with sample id in rows and variables in columns
tSNE.usePCA	whether perform PCA before tSNE (default: T)
tSNE.perplexity	perplexity parameter of tSNE (default: 30)
method	method to be used. one of "Rtsne" and "FIt-SNE" (default: "Rtsne")
n.cores	integer; number of cores used, if NULL it will be determined automatically (default: NULL)
out.prefix	character; output prefix (default: NULL)
...	parameters passed to Rtsne or fftRtsne

Value

If successful same as the return value of Rtsne(); otherwise NULL

Japrin/sscClust documentation built on Dec. 15, 2022, 1:04 p.m.