Description Usage Arguments Value Examples

View source: R/differential_methylation.R

This subroutine uses Euclidean distance to group CpGs and then combine p-values for each segment. The function performs DML test first if cf is NULL. It groups the probe testing results into differential methylated regions in a coefficient table with additional columns designating the segment ID and statistical significance (P-value) testing the segment.

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`betas` |
beta values for distance calculation |

`sample.data` |
data frame for sample information, column names are predictor variables (e.g., sex, age, treatment, tumor/normal etc) and are referenced in formula. Rows are samples. |

`formula` |
formula |

`cf` |
coefficient table from diffMeth, when NULL will be computed from beta. If cf is given, sample.data and formula are ignored. |

`dist.cutoff` |
distance cutoff (default to use dist.cutoff.quantile) |

`seg.per.locus` |
number of segments per locus higher value leads to more segments |

`platform` |
EPIC or HM450 |

`refversion` |
hg38 or hg19 |

`...` |
additional parameters to DML |

coefficient table with segment ID and segment P-value

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