Description Usage Arguments Value

Iterative phasing and theta_hat estimation

1 |

`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. |

`sub_cells` |
A vector of cell names for the cells used to estimate the phases. |

`seed` |
An integer of random seed number for EM initialization. |

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.

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