getPotentialDIMP {MethylIT} | R Documentation |

This function perform a selection of the cytosine sites carrying the potential methylation signal. The potential signals from controls and treatments are used as prior classification in further step of signal detection.

getPotentialDIMP(LR, nlms = NULL, div.col, dist.name = "Weibull2P", absolute = FALSE, alpha = 0.05, tv.col = NULL, tv.cut = NULL, min.coverage = NULL, hdiv.col = NULL, hdiv.cut = NULL)

`LR` |
An object from 'InfDiv' class. This obejct is previously obtained
with function |

`nlms` |
A list of distribution fitted models (output of 'fitNonlinearWeibullDist' function) or NULL. If NULL, then empirical cumulative distribution function is used to get the potential DIMPs. |

`div.col` |
Column number for divergence variable is located in the meta-column. |

`dist.name` |
name of the distribution to fit: Weibull2P (default: "Weibull2P"), Weibull three-parameters (Weibull3P), gamma with three-parameter (Gamma3P), gamma with two-parameter (Gamma2P), generalized gamma with three-parameter ("GGamma3P") or four-parameter ("GGamma4P"), the empirical cumulative distribution function (ECDF) or "None". |

`absolute` |
Logic (default, FALSE). Total variation (TV, the difference of methylation levels) is normally an output in the downstream MethylIT analysis. If 'absolute = TRUE', then TV is transformed into |TV|, which is an information divergence that can be fitted to Weibull or to Generalized Gamma distribution. So, if the nonlinear fit was performed for |TV|, then absolute must be set to TRUE. |

`alpha` |
A numerical value (usually alpha < 0.05) used to select cytosine sites k with information divergence (DIV_k) for which Weibull probability P[DIV_k > DIV(alpha)]. |

`tv.col` |
Column number for the total variation to be used for filtering cytosine positions (if provided). |

`tv.cut` |
If tv.cut and tv.col are provided, then cytosine sites k with abs(TV_k) < tv.cut are removed before to perform the ROC analysis. |

`min.coverage` |
Cytosine sites with coverage less than min.coverage are discarded. Default: 0 |

`hdiv.col` |
Optional. A column number for the Hellinger distance to be used for filtering cytosine positions. Fedault is NULL. |

`hdiv.cut` |
If hdiv.cut and hdiv.col are provided, then cytosine sites k with hdiv < hdiv.cut are removed. |

The potential signals are cytosine sites k with information divergence (DIV_k) values greater than the DIV(alpha = 0.05). The value of alpha can be specified. For example, potential signals with DIV_k > DIV(alpha = 0.01) can be selected. For each sample, cytosine sites are selected based on the corresponding fitted Weilbull distribution model that has been supplied.

A list of GRanges objects, each GRanges object carrying the selected cytosine sites and and the Weibull probability P[DIV_k > DIV(alpha)].

num.points <- 1000 HD <- GRangesList( sample1 = makeGRangesFromDataFrame( data.frame(chr = "chr1", start = 1:num.points, end = 1:num.points, strand = '*', hdiv = rweibull(1:num.points, shape = 0.75, scale = 1)), keep.extra.columns = TRUE)) nlms <- nonlinearFitDist(HD, column = 1, verbose = FALSE) getPotentialDIMP(LR = HD, nlms = nlms, div.col = 1, alpha = 0.05)

[Package *MethylIT* version 0.3.1 ]