dim_red_scMethrix: Reduces dimensionality (tSNE, UMAP, PCA, or custom)

Description Usage Arguments Details Value See Also Examples

View source: R/scMethrix_dimensionality.R

Description

Reduces dimensionality (tSNE, UMAP, PCA, or custom)

Usage

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dim_red_scMethrix(
  scm,
  assay = "score",
  type = c("tSNE", "UMAP", "PCA"),
  var = c("top", "rand"),
  top_var = 1000,
  perplexity = 30,
  verbose = FALSE,
  n_components = 2,
  n_neighbors = 15,
  ...
)

Arguments

scm

scMethrix; Input scMethrix object

assay

string; The assay to use. Default is 'score'

type

string; the type of imputation "tSNE","UMAP", or "PCA"

var

strning; Choose between random CpG sites ('rand') or most variable CpGs ('top'). Default 'top'

top_var

integer; Number of variable CpGs to use. Default 1000 Set it to NULL to use all CpGs (which is not recommended due to memory requirements).

perplexity

numeric; Perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1, see details for interpretation)

verbose

boolean; flag to output messages or not

n_components

integer; Number of components to use

n_neighbors

integer; number of nearest neighbors for UMAP

...

Other arguments that can be passed to Rtsne

Details

Does reduction stuff

Value

scMethrix object with reducedDim assay

See Also

plot_dim_red() for plotting

Examples

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data('scMethrix_data')

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.