prfreq

[…] for processing genotypes and allele frequency spectra., to test for the influence of selection on the allele frequency spectrum of cnvs, we used a poisson random field approach implemented in prfreq , which evaluates the expected allele frequency distributions given different demographic and selection models. we compared the estimates of the scaled selection coefficient γ of cnvs (both […]

[…] of rare variation in human populations (; ). another class of methods to infer the dfe uses the poisson random field (prf) approach (; ; ; ; ; ). this approach has been implemented in the program prfreq (), but that implementation becomes numerically unstable when applied to samples larger than a few hundred individuals. the program ∂a∂i () uses a similar framework, but implementing a dfe […]

[…] the frequencies of cnvs versus snps, we estimated the scaled coefficient of natural selection γ and 95% confidence intervals (ci) using the poisson random field approach implemented in the program prfreq . whereas intergenic snps appear to be near neutral (γ = 0.2, ci 0.1 to 0.3), purifying selection may be shaping the distribution of both deletions (γ = −2.2, ci −2.0 to −2.5) and duplications […]

[…] site-frequency spectra from the yri population in the 1000 genomes project as a neutral standard to fit a gamma distribution of selective effects using the population expansion model in the prfreq software . the demographic parameters of tau (scaled time since non-stationary population dynamics) and omega (ratio of ancestral to current population size) derived from african-american data […]

[…] distribution of selection coefficients consistent with the observed non-synonymous frequency spectrum using a modified version of the program dadi that incorporates the functionality of the program prfreq . the expected sfs was generated based on 2000 values of the scaled selection coefficient (γ = 2 ns) distributed uniformly on a logarithmic scale between γ = −10−6 and γ = −2000, along with γ = […]

[…] the french and french-canadian populations. first, we estimated the demographic parameters and the population selection parameter (γ = ne(s)) using the poisson random fields method implemented in prfreq . to estimate population demographic parameters, we used synonymous sites to test different demographic models and we find a significantly better fit for models that include a bottleneck […]