geovar.GeoVar

class geovar.GeoVar(bins=[(0, 0), (0, 0.05), (0.05, 1.0)])

GeoVar object that performs binning of allele frequencies.

__init__(bins=[(0, 0), (0, 0.05), (0.05, 1.0)])

Object to perform binning of allele frequencies.

Parameters:

• bins (list) – list of tuples

• categories. (containing allele frequency) –

Methods

__init__([bins])	Object to perform binning of allele frequencies.
add_freq_mat(freq_mat_file)	Adding an allele frequency table (see example notebook for format).
count_geovar_codes()	Count the number of unique GeoVar codes in a dataset.
generate_bins([bins])	Define new bins for each allele frequency categorization.
geovar_binning()	Compute the GeoVar codes for each variant across each population.
geovar_codes_streaming(freq_mat_file)	Version of GeoVar code generation algorithm that streams through file to avoid memory overflow.