comptSNE: Computing tSNE

In DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

Computing tSNE

Description

This function is used to compute the t-Distributed Stochastic Neighbor Embedding (t-SNE).

Usage

comptSNE(
  object,
  rseed = NULL,
  max_iter = 5000,
  epoch = 500,
  quiet = FALSE,
  ...
)

## S4 method for signature 'DISCBIO'
comptSNE(
  object,
  rseed = NULL,
  max_iter = 5000,
  epoch = 500,
  quiet = FALSE,
  ...
)

Arguments

object	DISCBIO class object.
rseed	Random integer to to yield reproducible maps across different runs
max_iter	maximum number of iterations to perform.
epoch	The number of iterations in between update messages.
quiet	if 'TRUE', suppresses intermediate output
...	other parameters to be passed to 'tsne::tsne'

Value

The DISCBIO-class object input with the tsne slot filled.

Examples

sc <- DISCBIO(valuesG1msTest) # changes signature of data
sc <- Clustexp(sc, cln = 2) # data must be clustered before plottin
sc <- comptSNE(sc, max_iter = 30)
head(sc@tsne)

DIscBIO documentation built on Nov. 6, 2023, 5:08 p.m.