copy_number_variation

pylluminator.cnv.copy_number_variation(samples: ~pylluminator.samples.Samples, sample_label: str, normalization_sample_labels: str | list[str] | None = None) -> (<class 'pyranges.core.pyranges_main.PyRanges'>, <class 'pandas.core.frame.DataFrame'>, <class 'pandas.core.frame.DataFrame'>)

Perform copy number variation (CNV) and copy number segmentation for a sample

Parameters:

  • samples (Samples) – samples to be analyzed

  • sample_label (str) – name of the samples to calculate CNV of.

  • normalization_sample_labels (str | list[str]) – names of the samples to use for normalization, that have to be part of the passed Samples object. If empty (default), default normalization samples will be loaded from a database - but this only work for EPIC/hg38 and EPICv2/hg38; for other array versions, you need to provide samples. Default []

Returns:

a tuple with : the bins coordinates, the bins signal, the segments

Return type:

tuple[pyranges.PyRanges, pandas.DataFrame, pandas.DataFrame]