copy_number_segmentation

pylluminator.cnv.copy_number_segmentation(samples: ~pylluminator.samples.Samples, cnv_df: ~pandas.core.frame.DataFrame, cnv_column_name: str) -> (<class 'pyranges.core.pyranges_main.PyRanges'>, <class 'pandas.core.frame.DataFrame'>, <class 'pandas.core.frame.DataFrame'>)

With the output dataframe of copy_number_variation, group the genome in segments with similar CNV.

Parameters:

• samples (Samples) – samples to be analyzed

• cnv_df (pandas.DataFrame) – dataframe with the CNV information

• cnv_column_name – name of the CNV column in the dataframe (it usually corresponds to the sample name used

for CNV calculation). :type cnv_column_name: str

Returns:

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

Return type:

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