dimReduce: Get lower dimension embedding

In BIMSBbioinfo/netSmooth: Network smoothing for scRNAseq

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

BIMSBbioinfo/netSmooth documentation built on Dec. 24, 2019, 8:08 p.m.