runUMAP: Cluster matrix data by UMAP

In karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels

Cluster matrix data by UMAP

Description

Analyzes matrix data by UMAP and saves results to reducedDims slot of TapestriObject.

Usage

runUMAP(
  TapestriExperiment,
  alt.exp = "alleleFrequency",
  assay = NULL,
  use.pca.dims = TRUE,
  pca.dims = NULL,
  ...
)

Arguments

TapestriExperiment	TapestriExperiment object
alt.exp	Character, altExp to use, NULL uses top-level/main experiment. Default "alleleFrequency".
assay	Character, assay to use. NULL (default) uses first-indexed assay. Not used when use.pca.dims = TRUE.
use.pca.dims	Logical, if TRUE, uses experiment PCA, otherwise uses assay data. Default TRUE.
pca.dims	Numeric, indices of PCs to use in UMAP. Default NULL.
...	Additional parameters to pass to umap::umap(), e.g. for configuration (see umap::umap.defaults()).

Value

TapestriExperiment with UMAP embeddings saved to reducedDims slot of altExp.

Examples

tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
tap.object <- runPCA(tap.object, alt.exp = "alleleFrequency")
tap.object <- runUMAP(tap.object, pca.dims = 1:3)

karyotapR documentation built on Sept. 8, 2023, 5:07 p.m.