Description Usage Arguments Details Value Examples

Function that given observed count data along a known haplotype returns a maximum likelihood estimate of the underlying haplotype frequency.

1 2 | ```
maxLogLikelihoodCalculator1s(lociHapACounts, lociTotalCounts,
lociHapANoASEProbs, lociRhos, checkArgs = FALSE)
``` |

`lociHapACounts` |
counts of haplotype A-supporting reads at individual loci. Must be a vector of non-negative integers. |

`lociTotalCounts` |
total read counts of at individual loci. Must be a vector of positive integers. |

`lociHapANoASEProbs` |
probabilities of observing haplotype A-supporting reads at individual loci under conditions of no ASE (e.g., vector with all entries set to 0.5, if there is no pre-existing allelic bias at any locus). Must be a vector with entries >0 and <1. |

`lociRhos` |
dispersion parameters of beta distribution at individual loci (set to 0 if the read count-generating distribution at the locus is binomial). Must be a numeric vector with entries >=0 and <1. |

`checkArgs` |
single boolean specifying whether arguments should be checked for adherence to specifications. DEFAULT: FALSE |

Given observed read counts supporting hapltoype A at a collection of loci, the total read counts at those loci, the probablities of observing haplotype A-supporting reads under conditions of no ASE and the dispersion parameters, this function returns a maximum likelihood estimate of the true underlying frequency of haplotype A as well as corresponding value of log-likelihood.

a list with two elements: maximum (MLE of haplotype A frequency) and objective (loglikelihood at MLE). These are the two elements that are output by the optimize() function, which is used internally by the maxLogLikelihoodCalculator1s.

1 |

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