add beneficial-containing DFE

[petrelharp]

For instance we could get it from Zhen et al in Genome Research (including Lohmueller); see citations in that paper.
https://genome.cshlp.org/content/31/1/110.abstract

[petrelharp]

@RyanGutenkunst

[klohmueller]

For a DFE with positive selection in humans—we could use this one from Table S6 of Zhen et al. (2021). This DFE is for nonsynonymous mutations. We inferred 1.55% of nonsynonymous mutations were positively selected in humans with a s of 0.0001124605. The remaining nonsynonymous mutations came from a DFE for negative selection (parameters for this are in Table S3). The shape parameter is 0.19 and the scale (beta) in terms of s is 0.074.

[andrewkern]

another possibility for a beneficial DFE that @petrelharp mentioned was @mufernando's recent paper in GENETICS.

@petrelharp -- what species were you thinking we might apply that to? humans? chimps? all apes?

[petrelharp]

For a DFE with positive selection in humans—we could use this one from Table S6 of Zhen et al. (2021). This DFE is for nonsynonymous mutations. We inferred 1.55% of nonsynonymous mutations were positively selected in humans with a s of 0.0001124605. The remaining nonsynonymous mutations came from a DFE for negative selection (parameters for this are in Table S3). The shape parameter is 0.19 and the scale (beta) in terms of s is 0.074.

Okay - so, this starts from Huber et al, so this is Gamma_H17 but modified so that a proportion of the nonsynonymous mutations have a (single, fixed) positive selection coefficient as @klohmueller says above.

[petrelharp]

Note we did already have one positive-containing DFE.