API

pylluminator.annotations	Classes and methods to handle genome metadata : Illumina manifest with probes information, Genome version (hg38, mm10...), Array types (EPIC, MSA...), Channels (Red/Green).
pylluminator.cnv	Functions to compute the Copy Number Variation (CNV), ie detect changes in the number of copies on a particular region of the genome, and splits the genome in segments with similar CNV.
pylluminator.dm	Functions used to compute DMRs (Differentially Methylated Regions) and DMPs (Differentially Methylated Probes).
pylluminator.mask	Classes that handles probes masks
pylluminator.quality_control	Functions to give an insight on a single Sample object probes values by calculating and printing some reference statistics.
pylluminator.read_idat	Functions to parse .idat files.
pylluminator.sample_sheet	Functions to generate sample sheets from idat files, or parse a provided sample sheet
pylluminator.samples	Class that holds a collection of Sample objects and defines methods for batch processing.
pylluminator.stats	Mathematical tools for samples processing
pylluminator.utils	Tools for file handling, logger parametrization, dataframe manipulation...
pylluminator.visualizations	Functions to plot data from Samples object or DMPs/DMRs dataframes