karyotapR (version 1.0.1)

getGMMBoundaries: 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")

Value

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

Arguments

TapestriExperiment

TapestriExperiment object.

chromosome.scope

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

Examples

# \donttest{
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"
)
# }