Run sample multidimensional scaling — reduce_mds • bulkMAE

Uses limma::plotMDS() with plot = FALSE and returns the native MDS object without opening a graphics device.

Usage

reduce_mds(
  x,
  experiment,
  assay,
  features = NULL,
  top = 500,
  gene_selection = "pairwise",
  ...
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
assay: Assay name or one-based assay index.
features: Optional feature subset.
top: Number of leading features used by plotMDS.
gene_selection: Feature-selection rule accepted by plotMDS.
...: Additional arguments passed to limma::plotMDS().

Value

A native limma MDS object.