epitome.conversion.RegionConversion

class epitome.conversion.RegionConversion(base_bed, compare_bed)

Class for dealing with genomic region conversions. In Epitome, we often have to join a user’s query genomic regions with a larger region set (i.e. EpitomeDataset regions). This class performs two functions: converting a user defined list of genomic regions to a vector that matches a larger bed file, and converting Epitome predictions back to the original bed regions.

__init__(base_bed, compare_bed)

Initialization function for RegionConversion class.

Parameters

• base_bed (str|pyranges) – either path to bed file or indexed pyranges base object

• compare_bed (str|pyranges) – either path to bed file or indexed pyranges comparison object

Methods

__init__(base_bed, compare_bed)	Initialization function for RegionConversion class.
compare_df()	Gets genomic regions ordered by idx
convert(regions)	Converts a bed file to indexed pyranges.
get_base_overlap_index()	Returns index of locations in base where there is supporting data in both base and compare
get_binary_vector([vector])	Finds indices in base that overlap compare and return vector matching regions.
merge(matrix[, axis])	Groups matrix shaped by base pyranges and calculates new predictions by taking the mean to match the shape of compare pyranges.