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)#

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)#

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:

GeoData

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.

Parameters:

matrix (Union[str, DataFrame]) – Methylation matrix as a DataFrame or the path to the CSV file containing the matrix.

Returns:

An instance of GeoData with the methylation data loaded and metadata initialized.

Return type:

GeoData

Examples using biolearn.data_library.GeoData#

“Epigenetic Clocks” in GEO Data

"Epigenetic Clocks" in GEO Data

Down Syndrome Epigenetic Plotting

Down Syndrome Epigenetic Plotting

Performing custom imputations

Performing custom imputations

“Deconvolution Example”

"Deconvolution Example"