Description Usage Arguments Examples

This function returns the GPHMM probability that a read x could have been sequenced from a reference sequence y.

1 | ```
calculategphmm(x, y, tau, pp, qX, qY, dX, dY, eX, eY)
``` |

`x` |
string, with the sequence of the read. |

`y` |
string, with the sequence of the reference. |

`tau` |
double, probability to transition from any state to end state. |

`pp` |
matrix, emission probabilities in the M state. |

`qX` |
vector, emission probabilities in the insertion state. |

`qY` |
vector, emission probabilities in the deletion state. |

`dX` |
double, transition probability from the M to the insertion state. |

`dY` |
double, transition probability from the M to the deletion state. |

`eX` |
double, transition probability from the insertion to the insertion state. |

`eY` |
double, transition probability from the deletion to the deletion state. |

1 2 3 4 5 6 7 8 9 10 | ```
param <- initializeGphmm()
tau <- param[['tau']]
pp <- param[['pp']]
qX <- param[['qX']]
qY <- param[['qY']]
dX <- 1/(1+exp(-sum(param[['deltaX']] * c(1, 20))))
dY <- 1/(1+exp(-sum(param[['deltaY']] * c(1, 20))))
eX <- param[['epsX']]
eY <- param[['epsY']]
calculategphmm('ATCG', 'ATGG', tau, pp, qX, qY, dX, dY, eX, eY)
``` |

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