rfmix_reader.generate_tagore_bed

rfmix_reader.generate_tagore_bed(loci, rf_q, admix, sample_num, verbose=True)[source]

Generate a BED (Browser Extensible Data) file formatted for TAGORE visualization.

This function processes genomic data and creates a BED file suitable for visualization with TAGORE (https://github.com/jordanlab/tagore).

Parameters:

  • loci (DataFrame) – A DataFrame containing genomic loci information.

  • rf_q (DataFrame) – A DataFrame containing recombination fraction quantiles.

  • admix (Array) – An array of admixture proportions.

  • sample_num (int) – The sample number to process.

  • verbose (bool, optional) – If True, print progress information. Defaults to True.

Returns:

A DataFrame in BED format, annotated and ready for TAGORE

visualization.

Return type:

DataFrame

Note

This function relies on several helper functions: - admix_to_bed_chromosome: Converts admixture data to BED format for a

specific chromosome.

  • _string_to_int: Converts specific columns in the BED DataFrame to

    integer type (interal function).

  • _annotate_tagore: Adds annotation columns required for TAGORE

    visualization (internal function).