callAlleleSpecificCNfromHSCN: Call allele specific copy number in single cell datasets

In shahcompbio/signals: Single Cell Genomes with Allele Specificity

Call allele specific copy number in single cell datasets

Description

Call allele specific copy number in single cell datasets

Usage

callAlleleSpecificCNfromHSCN(
  hscn,
  eps = 1e-12,
  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

Details

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

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))

shahcompbio/signals documentation built on Jan. 11, 2025, 2:20 a.m.