Description Usage Arguments Details Value Examples

Function that adjusts true underlying allele frequency for pre-existing allelic bias to produce actual generating probability of observing allele-supporting read

1 |

`trueAF` |
true underlying allele frequency. Must be a single number >=0 and <=1. |

`noASEAF` |
probability of observing allele-supporting read under conditions of no ASE. Must be a vector of numbers >0 and <1. |

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

Given true underlying allele frequency AF and probability of observing reads supporting that allele under conditiosn of no ASE (P(allele, noASE)), it calculates the generating probability for observed allele-supporting reads as P(allele-supporting read)=AF*P(allele, noASE)/(AF*P(allele, noASE) + (1-AF)*(1-P(allele, noASE))).

a vector of generating probabilities of the same length as noASEAF

1 2 3 4 | ```
MBASED:::getPFinal(trueAF=1, noASEAF=seq(0.1, 0.9, by=0.1)) ## is always 1
MBASED:::getPFinal(trueAF=0, noASEAF=seq(0.1, 0.9, by=0.1)) ## is always 0
MBASED:::getPFinal(trueAF=0.3, noASEAF=0.5) ## no pre-existing allelic bias
c(MBASED:::getPFinal(trueAF=0.3, noASEAF=0.9), MBASED:::getPFinal(trueAF=1-0.3, noASEAF=1-0.9)) ## strong pre-existing allelic bias
``` |

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