getGMMBoundaries: Calculate decision boundaries between components of copy...

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

Calculate decision boundaries between components of copy number GMMs

Description

Calculate decision boundaries between components of copy number GMMs

Usage

getGMMBoundaries(TapestriExperiment, chromosome.scope = "chr")

Arguments

TapestriExperiment	TapestriExperiment object.
chromosome.scope	"chr" or "arm", for using models for either whole chromosomes or chromosome arms. Default "chr".

Value

tibble containing boundary values of GMMs for each feature.id.

Examples

tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
tap.object <- calcNormCounts(tap.object)
control.copy.number <- generateControlCopyNumberTemplate(tap.object,
  copy.number = 2,
  sample.feature.label = "cellline1"
)
tap.object <- calcCopyNumber(tap.object,
  control.copy.number,
  sample.feature = "test.cluster"
)
tap.object <- calcSmoothCopyNumber(tap.object)
tap.object <- calcGMMCopyNumber(tap.object,
  cell.barcodes = colnames(tap.object),
  control.copy.number = control.copy.number,
  model.components = 1:5
)

boundaries <- getGMMBoundaries(tap.object,
  chromosome.scope = "chr"
)

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