rephasebins: Rephase haplotype copy number

In shahcompbio/signals: Single Cell Genomes with Allele Specificity

Rephase haplotype copy number

Description

This function implements 2 rephasing algorithms. The first mindist, implementthe dynamic programming algorithm to rephase haplotype copy number first described in CHISEL. The objective is to find the phase that minimizes the number of copy number events. The second LOH finds cells with whole chromosome losses and assumes this was a single event and rephases all the bins relative to this.

Usage

rephasebins(
  cn,
  chromosomes = NULL,
  method = "mindist",
  whole_chr_cutoff = 0.9,
  ncells = 1,
  clusterfirst = FALSE,
  cl = NULL
)

Arguments

cn	either a hscn object from callHaplotypeSpecificCN or a dataframe with haplotype specific copy number ie the data slot in an hscn object
chromosomes	vector specifying which chromosomes to phase, default is NULL whereby all chromosomes are phased
method	either mindist or LOH
ncells	default 1
clusterfirst	Whether to cluster cells and perform rephasing on clusters rather than cells
cl	Precomputed clustering object from umap_clustering

Value

Either a new hscn object or a dataframe with rephased bins depdending on the input

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