Description Usage Arguments Value Author(s) See Also Examples

View source: R/compareREDseq.R

For early stage experiment without replicates, compareREDseq outputs differentially cut RE sites between two experimental conditions using Fisher's Exact Test.

1 2 | ```
compareREDseq(REsummary, col.count1 = 2, col.count2 = 3, multiAdj = TRUE,
multiAdjMethod = "BH", maxP = 1, minCount = 1)
``` |

`REsummary` |
A matrix with a RE id column, 2 count/weight column, see examples |

`col.count1` |
The column where the total count/weight for the 1st experimental condition is |

`col.count2` |
The column where the total count/weight for the 2nd experimental condition is |

`multiAdj` |
Whether apply multiple hypothesis testing adjustment, TURE or FALSE |

`multiAdjMethod` |
Multiple testing procedures, for details, see mt.rawp2adjp in multtest package |

`maxP` |
The maximum p-value to be considered to be significant |

`minCount` |
For a RE site to be included, the tag count from at least one of the experimental condictions >= minimumCount |

`p.value` |
the p-value of the test |

`*.count` |
weight/count from the input column col.count1 and col.count2 |

`*.total` |
total weight/count from input column col.count1 and col.count2 |

`REid` |
the id of the restriction enzyme from the input |

`odds.ratio` |
an estimate of the odds ratio for 2nd experimental condition vs. 1st experimental condition |

`*.adjusted.p.value` |
applicable if multiAdj=TRUE, adjusted p.value using the method * specified in multiAdjMethod |

Lihua Julie Zhu

binom.test.REDseq

1 2 3 4 |

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