annotations

Classes and methods to handle genome metadata : Illumina manifest with probes information, Genome version (hg38, mm10…), Array types (EPIC, MSA…), Channels (Red/Green).

The default annotation data is read from pylluminator-data package, but you can add your own annotations.

Functions

detect_array(probe_count)	Auto-detect the type of array of a sample, depending on the number of probes in the .idat files.
get_or_download_annotation_data(...)	Check if the csv file exists, and if not download it from the given link and save it in the output folder under the same name.

Classes

Annotations(array_type, genome_version[, name])	This class contains all the metadata associated with a certain genome version (HG39, MM10...) and array type (EPICv2, 450K...).
ArrayType(*values)	Names of the different array types supported.
Channel(*values)	Probes measure either a red or green fluorescence.
GenomeInfo(name, genome_version)	Additional genome information provided by external files, downloaded from illumina-data.
GenomeVersion(*values)	Names of the different genome versions supported.