Description Arguments Author(s)

parameters name and their descriptions

`methReads` |
The matrix |

`totalReads` |
The matrix |

`methLevels` |
The matrix |

`methStates` |
The matrix |

`rowRanges` |
A |

`colData` |
Object of class |

`metadata` |
An optional |

`object` |
A |

`value` |
An integer matrix |

`obj1` |
A |

`obj2` |
A |

`files` |
A character list |

`file` |
A character |

`name` |
A character list |

`MaxK` |
An integer value |

`MaxEmiter` |
An integer value |

`epsEM` |
A positive numeric value |

`useweight` |
A logical value |

`mc.cores` |
An integer greater than 0 |

`nburn` |
An integer value |

`nthin` |
An integer value |

`nsamp` |
An integer value |

`formula` |
A formula |

`FDRthreshold` |
A numeric value |

`Methylthreshold` |
A numeric value |

`...` |
other possible parameters |

`col` |
A character vector indicating which colors to alternate. |

`chrlabs` |
A character vector equal to the number of chromosomes
specifying the chromosome labels (e.g., |

`suggestiveline` |
Where to draw a "suggestive" line. Default -log10(1e-5). Set to FALSE to disable. |

`genomewideline` |
Where to draw a "genome-wide sigificant" line. Default -log10(5e-8). Set to FALSE to disable. |

`highlight` |
A character vector of SNPs in your dataset to highlight. These SNPs should all be in your dataset. |

`logp` |
If TRUE, the -log10 of the p-value is plotted. It isn't very useful to plot raw p-values, but plotting the raw value could be useful for other genome-wide plots, for example, peak heights, bayes factors, test statistics, other "scores," etc. |

`annotatePval` |
If set, SNPs below this p-value will be annotated on the plot. |

`annotateTop` |
If TRUE, only annotates the top hit on each chromosome that is below the annotatePval threshold. |

Farhad Shokoohi <[email protected]>

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