sumstats
Utilities for working with GWAS summary statistics
This is a package on pypi so you can get it with pip install sumstats
Fine mapping
If inputs are p-values, minor allele frequency, and sample size, first calculate natural log bayes factors and then calculate the PPA's.
To set things up:
import math
import sumstats
N = <sample size>
p_values = <p_values of variants in fine-mapping region>
mafs = <minor allele frequencies of variants in fine-mapping region>
To calculate natural log bayes factors or "lnbf":
lnbfs = [sumstats.approx_lnbf(pval=p, freq=maf, sample_size=N) for p, maf in zip(p_values, mafs)]
To caluclate posterior probability of association:
normalizing_coefficient = sumstats.log_sum(lnbfs)
ppa = [math.exp(lnbf - normalizing_coefficient) for lnbf in lnbfs]
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Release files for sumstats 0.1.2
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