Description Usage Arguments Value Author(s) See Also Examples

These functions are used to generate the parameters for different nucleosome positioning related features.

1 2 3 4 5 6 7 8 9 10 | ```
stableFeature(start, minDist = 175, weight = seq(0.1, 1, by = 0.1),
shift = c(0, 5, 10), ratio = seq(0, 4, by = 0.25),
stability = seq(0.1, 5, by = 0.1), weightProb, shiftProb,
ratioProb, stabilityProb, ...)
phasedFeature(minDist = 175, length = seq(1000, 10000, by = minDist),
meanDist = minDist:300, lengthProb, meanDistProb, start, ...)
fuzzyFeature(start, length = seq(1000, 10000, by = 1000),
meanDist = 175:400, lengthProb, meanDistProb, ...)
nfrFeature(start, length = seq(50, 500, by = 10),
weight = seq(0.1, 1, by = 0.1), lengthProb, weightProb, ...)
``` |

`start` |
Start location of feature on chromosome. |

`minDist` |
Minimum distance between nucleosomes. |

`length` |
A numeric vector giving possible values for the length of the feature. |

`meanDist` |
A numeric vector giving possible values for the mean distance between nucleosomes. |

`weight` |
A numeric vector giving possible values for the weight of the feature. |

`shift` |
A numeric vector giving possible values for the distance between favoured positions of stable nucleosomes. |

`ratio` |
A numeric vector giving possible values for the ratio between probabilities for alternative and central position of stable nucleosomes. |

`stability` |
A numeric vector giving possible values for the stability of stable nucleosomes. |

`lengthProb` |
Length distribution of feature. This corresponds to the state duration distribution of the underlying generating model. |

`meanDistProb` |
Distribution of mean distances between nucleosomes. |

`weightProb` |
Distribution of feature weights. |

`shiftProb` |
Distribution of distances between favoured positions of stable nucleosome. |

`ratioProb` |
Ratio distribution. |

`stabilityProb` |
Stability distribution. |

`...` |
Further arguments (currently ignored). |

A list of parameters for the corresponding feature type. These parameters are later used to compute nucleosome densities.

Peter Humburg

1 | ```
feature <- stableFeature(200)
``` |

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