Description Usage Arguments Value Author(s) Examples

View source: R/RcppExports.R View source: R/rjmcmcMethodsIntern.R

Function that calls the core of the nucleosome positioning mapping function that is implemented in C++.

1 2 3 | ```
rjmcmcNucleo(startPosForwardReads, startPosReverseReads, nbrIterations, kMax,
lambda, minInterval, maxInterval, minReads = 5L,
adaptIterationsToReads = TRUE, vSeed = -1)
``` |

`startPosForwardReads` |
a |

`startPosReverseReads` |
a |

`nbrIterations` |
a positive |

`kMax` |
a positive |

`lambda` |
a positive |

`minInterval` |
a |

`maxInterval` |
a |

`minReads` |
a positive |

`adaptIterationsToReads` |
a |

`vSeed` |
a |

a `list`

containing:

k a

`integer`

, the number of nucleosomes.k_max a

`integer`

, the maximum number of nucleosomes obtained during the iteration process.it a

`vector`

of`integer`

of length`k`

, the variance of the forward reads for each nucleosome.nbState a

`integer`

, the number of changes of state.mu a

`matrix`

of`numeric`

with`k_max`

columns and`nbState`

row containing, in each row, the`mu`

values associated the the state identified by the row number.muHat a

`matrix`

of`numeric`

with`k_max`

columns and`k_max`

rows containing, in each row, the mean`mu`

values associated the number of nucleosomes detected. The row number corresponds to the number of nucleosomes detected.nbK a

`vector`

of length`k_max`

containing`integer`

, the number of iterations which detected a specific number of nucleosomes. The position in the vector correspond to the number of nucleosomes.

Pascal Belleau, Astrid Deschenes

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
data(reads_demo_01)
forward <- start(reads_demo_01[strand(reads_demo_01) == "+"])
reverse <- end(reads_demo_01[strand(reads_demo_01) == "-"])
## Run nucleosome positioning
result <- RJMCMCNucleosomes:::rjmcmcNucleo(
startPosForwardReads = forward,
startPosReverseReads = reverse,
nbrIterations = 1000, lambda = 2, kMax = 30,
minInterval = 146, maxInterval = 292, minReads = 5,
adaptIterationsToReads = TRUE, vSeed = -1)
## Print the final estimation of the number of nucleosomes
result$k
## Print the position of nucleosomes
result$mu
``` |

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