Iterative phasing and theta_hat estimation
Arguments
- ref_table
A SNP by cell read count matrix/ spare matrix for the reference alleles.
- alt_table
A SNP by cell read count matrix/ spare matrix for the alternative alleles.
- max_iter
An integer of maximum iteration number.
- seed
An integer of random seed number for EM initialization.
- phases
SNP phasing to use as priors
- tol
maximum liklihood stopping tolerance
Value
A list of estimated indicators (I_hat) for each SNP and estimated major haplotype proportion (theta_hat) for each cell in one region. I_hat is the phasing result indicating whether reference allele is on the major haplotype for each SNP. Theta_hat represents the CNV states for each cell. A cell is considered as a CNV carrier if its theta_hat depart from 0.5.