Call allele specific copy number in single cell datasets

Call allele specific copy number in single cell datasets

callAlleleSpecificCNfromHSCN(
  hscn,
  eps = 0.000000000001,
  maxCN = NULL,
  selftransitionprob = 0.95,
  progressbar = TRUE,
  ncores = 1,
  fillmissing = TRUE
)

Arguments

hscn

hscn object from callHaplotypeSpecificCN

eps

default 1e-12

maxCN

maximum copy number to infer allele specific states, default=NULL which will use the maximum state from CNbins

selftransitionprob

probability to stay in the same state in the HMM, default = 0.999, set to 0.0 for an IID model

progressbar

Boolean to display progressbar or not, default = TRUE, will only show if ncores == 1

ncores

Number of cores to use, default = 1

fillmissing

For bins with missing counts fill in values based on neighbouring bins

Value

allele specific copy number object which includes dataframe similar to input with additional columns which include

* `A` (Major allele copy number) * `B` (Minor allele copy number) * `state_AS_phased` (phased state of the form A|B ) * `state_AS` (mirrored state of the form A|B) * `LOH` (is bin LOH or not) * `state_phase` (state describing which is the dominant allele and whether it is LOH or not) * `state_BAF` (binned discretized BAF value calculated as B / (A + B))

Details

In the allele specific copy number inference A is always > B and state_AS_phased == state_AS