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.
- static convert_biolearn_to_standard_sex(s)#
Converts internal sex representation to the standard format.
- static convert_standard_to_biolearn_sex(val)#
Converts a standard sex value back to the internal representation.
- Parameters:
val (Any) – The standard sex value (0 for female, 1 for male, “NaN” or other for unknown).
- Returns:
Returns 1 for standard 0 (Female), 2 for standard 1 (Male), or 0 otherwise.
- Return type:
- save_csv(folder_path, name)#
Saves the GeoData instance to CSV files according to the DNA Methylation Array Data Standard V-2410.
- classmethod load_csv(folder_path, name, series_part='all')#
Loads a GeoData instance from CSV files according to the DNA Methylation Array Data Standard V-2410.
- Parameters:
- Returns:
A GeoData instance with metadata, methylation data, RNA, and protein data loaded.
- Return type:
