EM phasing of SNPs

Usage

phase_snps(
  snp,
  bins,
  max_iter = 50,
  sub_cells = NULL,
  phases = NULL,
  ncores = 1,
  min_snp_cov = 5,
  min_bin_snps = 5,
  tol = 0.001
)

Arguments

snp: SingleCellExperiment object containing hetSNPs as generated by read_vartrix
bins: GenomicRanges object containing bins (or segments) over which to perform phasing
max_iter: Maximum number of iterations for the EM
sub_cells: Subset cells when phasing
phases: Named vector of SNP phases.
ncores: Number of cores to parallelize over bins
min_snp_cov: Minimum total coverage per SNP to be used in phasing.
min_bin_snps: Minimum number of covered SNPs within a bin to be used.
tol: maximum liklihood stopping tolerance

Value

SingleCellExperiment object containing EM phased SNPs. Per bin values are stored in altExp(snp, 'em'). Per SNP results are appended to rowRanges(snp)