Note
This page is a reference documentation. It only explains the class signature, and not how to use it. Please refer to the user guide for the big picture.
biolearn.data_library.GeoData#
- class biolearn.data_library.GeoData(metadata, dnam=None, rna=None, protein=None)#
Represents genomic data with a focus on metadata and methylation data.
GeoData facilitates the organization and access to metadata and methylation data.
- metadata#
A pandas DataFrame where rows represent different samples and columns represent different data fields.
- Type:
DataFrame
- dnam#
A pandas DataFrame where columns represent different samples and rows represent different methylation sites.
- Type:
DataFrame
- __init__(metadata, dnam=None, rna=None, protein=None)#
Initializes the GeoData instance.
- Parameters:
metadata (DataFrame) – Metadata associated with genomic samples.
dnam (DataFrame) – Methylation data associated with genomic samples.
- copy()#
Creates a deep copy of the GeoData instance.
- Returns:
A new instance of GeoData with copies of the metadata and dnam DataFrames.
- Return type:
- quality_report(sites=None)#
Generates a quality control report for the genomic data, optionally filtered by specified methylation sites, and includes a detailed section reporting the missing percentage for each methylation site.
- Parameters:
sites (list, optional) – A list of methylation site identifiers to include in the report. If None, all sites are included.
- Returns:
- An object containing both detailed methylation data, a summary,
and a detailed section for missing percentages per site.
- Return type:
QualityReport
- classmethod from_methylation_matrix(matrix)#
Creates a GeoData instance from a methylation matrix which can be either a DataFrame directly or a path to a CSV file.
