Description Usage Arguments Value Examples

View source: R/runbumphunter.R

Run bumphunter to obtain DMRs (parameters stolen straight from bumphunter)

1 2 3 | ```
runbumphunter(methyl.mat, treatment, covariates, pickCutoff = TRUE,
pickCutoffQ = 0.975, maxGap = 300, smooth = FALSE, B = 250,
nullMethod = "bootstrap", n.core = 20)
``` |

`methyl.mat` |
matrix of samples by methylation |

`covariates` |
matrix (samples in rows, covar in column) |

`pickCutoff` |
Should bumphunter attempt to pick a cutoff using the permutation distribution? |

`pickCutoffQ` |
The quantile used for picking the cutoff using the permutation distribution. |

`maxGap` |
If cluster is not provided this maximum location gap will be used to define cluster via the clusterMaker function. |

`smooth` |
A logical value. If TRUE the estimated profile will be smoothed with the smoother defined by smoothFunction |

`B` |
An integer denoting the number of resamples to use when computing
null distributions. This defaults to 0. If permutations is supplied that
defines the number of permutations/bootstraps and B is ignored. |

`nullMethod` |
Method used to generate null candidate regions, must be one of <e2><80><98>bootstrap<e2><80><99> or <e2><80><98>permutation<e2><80><99> (defaults to <e2><80><98>permutation<e2><80><99>). However, if covariates in addition to the outcome of interest are included in the design matrix (ncol(design)>2), the <e2><80><98>permutation<e2><80><99> approach is not recommended. |

`n.core` |
number of cores to run in paralell |

annotated data frame; see bumphunter documentation for further explanation of output

1 | ```
DMS_annotated=annotateGenes(DMS)
``` |

ShanEllis/methylarking documentation built on May 10, 2017, 1:33 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.