This function discovers regions of enrichment in ChIP-seq data, using the method described in Hawkins RD. et al 2010 Cell Stem Cell.

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`rs.ip` |
A |

`rs.input` |
A |

`organism` |
The |

`chrs` |
An |

`ipWidth` |
Size in basepairs of the windows to use for the IP samples |

`inputWidth` |
Size in basepairs of the windows to use for the Input samples |

`preset` |
Either "small", "large" to use cutoffs described in Hawkins et al or |

`blockWidth` |
Number of adjacent blocks to consider at once |

`minBlocks` |
The minimum number of blocks required above |

`extend` |
Optional: whether to extend significant blocks until adjacent blocks are less than this value |

`cutoff` |
Optional: the cutoff to use to call regions. If left as |

`FDR` |
The target False Discovery Rate; If |

`nPermutations` |
The number of permutations of the data to determine the |

`nCutoffs` |
The number of different cutoffs to try to satisfy the |

`cutoffQuantile` |
The quantile of the RPKM to use as the maximum cutoff tried; a higher value will give lower resolution but may be needed if a |

`verbose` |
logical, whether to output commments of the processing |

`seq.len` |
If sequencing reads need to be extended, the fragment size to be used |

A `ChromaResults`

object.

Aaron Statham

`ChromaResults`

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