scATAC CBS CNV segmentation

Usage

segment_cnv(
  sce,
  assay_name,
  new_assay = paste(assay_name, "segment", sep = "_"),
  alpha = 0.2,
  nperm = 10,
  min.width = 2,
  undo.splits = "none",
  verbose = 0,
  bpparam = BiocParallel::SerialParam(),
  ...
)

Arguments

sce: A SingleCellExperiment object
assay_name: Name of the assay to segment
new_assay: Name of the new assay
alpha: significance levels for the test to accept change-points.
nperm: number of permutations used for p-value computation.
min.width: the minimum number of markers for a changed segment. The default is 2 but can be made larger. Maximum possible value is set at 5 since arbitrary widths can have the undesirable effect of incorrect change-points when a true signal of narrow widths exists.
undo.splits: A character string specifying how change-points are to be undone, if at all. Default is "none". Other choices are "prune", which uses a sum of squares criterion, and "sdundo", which undoes splits that are not at least this many SDs apart.
verbose: Verbosity
bpparam: BiocParallel Parameters
...: Additional parameters to pass to DNAcopy::segment

Value

A SingleCellExperiment object