get_dmr

pylluminator.dm.get_dmr(samples: Samples, dmps: DataFrame, contrast: str | list[str], dist_cutoff: float | None = None, custom_sheet: DataFrame | None = None, seg_per_locus: float = 0.5, probe_ids: None | list[str] = None) → DataFrame | None

Find Differentially Methylated Regions (DMR) based on euclidian distance between beta values

Parameters:

  • samples (Samples) – samples to use

  • dmps (pandas.DataFrame) – p-values and statistics for each probe, as returned by get_dmp()

  • contrast (str | list[str]) – contrast(s) to use for DMR detection

  • dist_cutoff (float | None) – cutoff used to find change points between DMRs, used on euclidian distance between beta values. If set to None (default) will be calculated depending on seg_per_locus parameter value. Default: None

  • custom_sheet (pandas.DataFrame | None) – a sample sheet to use. By default, use the samples’ sheet. Useful to filter out samples. Default: None

  • seg_per_locus (float) – used if dist_cutoff is not set : defines what quartile should be used as a distance cut-off. Higher values leads to more segments. Should be 0 < seg_per_locus < 1. Default: 0.5.

  • probe_ids (list[str] | None) – list of probe IDs to use. Useful to work on a subset for testing purposes. Default: None

Returns:

dataframe with DMRs or None if an error was raised

Return type:

pandas.DataFrame | None