dimReduce {netSmooth}R Documentation

Get lower dimension embedding

Description

Get lower dimension embedding

Usage

dimReduce(
  x,
  flavor = c("pca", "tsne", "umap"),
  k = 2,
  is.counts = TRUE,
  ntop = 500
)

Arguments

x

gene expresison matrix [GENES x SAMPLES]

flavor

the algorithm to use to obtain the dimensionality reduction must be in c('pca', 'tsne', 'umap')

k

the number of dimensions in the reduced dimension representation

is.counts

logical: is 'x' counts data

ntop

number of most variable genes to use for dimensionality reduction

Value

reduced dimensionality representation


[Package netSmooth version 1.13.0 Index]