Description Usage Arguments Value

Will perform permutations or bootstraps after methylaction() has been called. See also maPermMerge() and maPermFdr().

1 2 |

`ma` |
Output object from methylaction() |

`reads` |
Preprocessed reads/fragments data from getReads() |

`nperms` |
Number of permutation (or bootstrap) iterations to perform |

`combos` |
A matrix of pre-set combinations to use. Useful for smaller sample sizes where there are only a limited number of possible combinations. The row should have ncols = number of samples, and each row represents a re-ordering of samples into groups (where the groups will be set in the order they appear in the "samp" given to methylaction()) |

`save` |
If true, save an RData file of the permutations. These can be merged using maPermMerge(). Useful for running permutations across multiple computers or in a cluster environment. If FALSE, will return the permutation results. |

`perm.boot` |
If nperms > 0 and if TRUE, perform bootstrapping (sampling with replacement). Otherwise, perform permutations (sampling without permutations) |

`ncore` |
Number of parallel processes to use |

A list of DMRs arising from each permutation or bootstrap. Will save as an RData if save==TRUE.

jeffbhasin/methylaction documentation built on May 17, 2017, 3:59 p.m.

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.