Package overview
Main class Genie
The class Genie
is the main class of the genie
package. A Genie
object contains all data of a Genie release and the results of a re-annotation of mutations based on Illumina Connected Annotations (previously known as Nirvana).
How to create a Genie object
Other data classes
Other classes defined by the genie
package store the different data types
provided by the Genie consortium. Objects of the main class Genie
have
instances of these classes as members (attributes).
PatientInfo
: clinical data of patients.SampleInfo
: sample annotation.Mutations
: mutation data (SNVs and InDels) and mutation annotations.CNA
: copy number alteration data.Panel
: information about a single panel (annotation and content).PanelSet
: allPanel
s included in Genie.TestedPositions
: all positions tested by anyPanel
from thePanelSet
.Meta
: meta information on data files.
Configuration
The Configuration
class stores the names of original data files provided by
Genie and of auxiliary files derived from these original data files. The names
of these files are defined in a JSON configuration file that is part of the
genie
module. Users can provide a custom configuration file to override some
of the predefined file names if a new Genie version changes names.
The Configuration
class also provides some functions for loading data files
and auxiliary files as Pandas DataFrames. The data is read from cache files in
Parquet format. If a cache file does not exist yet, it is automatically created
from the original TSV file on the fly.
Details of data analysis
Please see the Analysis Details for a description how individual mutations are aggregated to gene level and how co-mutations are detected.