Description Usage Arguments Value Author(s) Examples

Obtain strand-specific peaks from GUIDE-seq

1 2 3 4 |

`gr` |
GRanges with cleavage sites, output from getUniqueCleavageEvents |

`window.size` |
window size to calculate coverage |

`step` |
step size to calculate coverage |

`bg.window.size` |
window size to calculate local background |

`min.reads` |
minimum number of reads to be considered as a peak |

`min.SNratio` |
minimum signal noise ratio, which is the coverage normalized by local background |

`maxP` |
Maximum p-value to be considered as significant |

`stats` |
Statistical test, default poisson |

`p.adjust.methods` |
Adjustment method for multiple comparisons, default none |

`peaks ` |
GRanges with count (peak height), bg (local background), SNratio (signal noise ratio), p-value, and option adjusted p-value |

`summarized.count` |
A data frame contains the same information as peaks except that it has all the sites without filtering. |

Lihua Julie Zhu

1 2 3 4 5 6 7 | ```
if (interactive())
{
data(uniqueCleavageEvents)
peaks <- getPeaks(uniqueCleavageEvents$cleavage.gr,
min.reads = 80)
peaks$peaks
}
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.