HLAfreq

HLAfreq allows you to download and combine HLA allele frequencies from multiple datasets, e.g. combine data from several studies within a country or combine countries. Useful for studying regional diversity in immune genes and, when paired with epitope prediction, estimating a population's ability to mount an immune response to specific epitopes.

Automated download of allele frequency data download from allele frequencies.net.

Details

Estimates are combined by modelling allele frequency as a Dirichlet distribution which defines the probability of drawing each allele. When combining studies their estimates are weighted as 2x sample size by default. Sample size is doubled as each person in the study contributes two alleles. Alternative weightings can be used for example population size when averaging across countries.

When selecting a panel of HLA alleles to represent a population, allele frequency is not the only thing to consider. Depending on the purpose of the panel, you should include a range of loci and supertypes (groups alleles sharing binding specificies).

Install

pip install HLAfreq

Minimal example

Download HLA data using makeURL() and getAFdata(). All arguments that can be specified in the webpage form are available, see help(HLAfreq.makeURL) for details (press q to exit).

import HLAfreq
base_url = HLAfreq.makeURL("Uganda", locus="A")
aftab = HLAfreq.getAFdata(base_url)

After downloading the data, it must be filtered so that all studies sum to allele frequency 1 (within tolerence). Then we must ensure that all studies report alleles at the same resolution. Finaly we can combine frequency estimates.

aftab = HLAfreq.only_complete(aftab)
aftab = HLAfreq.decrease_resolution(aftab, 2)
caf = HLAfreq.combineAF(aftab)

Detailed examples

For more detailed walkthroughs see HLAfreq/examples.

• Single country download and combine
• Multi-country download and combine, weight by population coverage
• Using priors
• Credible intervals

Docs

For help on specific functions view the docstring, help(function_name). Full documentation API at HLAfreq/docs created with pdoc3 in pdf mode.

Citation

In prep.