Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans

Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This can be thought of as a “linked selection signal\" that reflects the impact of selection varying according to the placement of functional regions and recombination rates along the genome. Previous work has shown that negative selection against the steady influx of new deleterious mutations into conserved regions is the predominant mode of selection in humans. However, the theoretic model that underpins these results, classic Background Selection theory, is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of the linked selection, which models the effects of weak draft created according to how polygenic additive fitness variance is distributed along the genome. We use a recent model that jointly predicts the equilibrium fitness variance and su..., These Python pickle files contain the model outputs from bgspy (http://github.com/vsbuffalo/bprime/) for the CADD 6%, CADD 8%, PhastCons Priority, and Feature Priority Models., , # Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans

## Usage Notes

All files are in in standard Python file formats. To load the pickle files, install the accompanying [bprime software available on GiHub](https://github.com/vsbuffalo/bprime).

Note that all TSV files here were written by analyses in Jupyter notebooks that are available on the [bprime GitHub page.](http://github.com/vsbuffalo/bprime)

## Files

### Model Fits

There are pickle files of model results, generated by `bgspy collect`.

* `cadd6__decode__altgrid.pkl`: CADD 6%
* `cadd8__decode__altgrid.pkl`: CADD 8%
* `CDS_genes_phastcons__decode__altgrid.pkl`: Feature Priority
* `phastcons_CDS_genes__decode__altgrid.pkl`: PhastCons Priority

## Files Produced by Sims

* `empiricalB_chr10__expansion_false__h_0.5__results.npz`: simulation B
\"empirical\" B maps for fixed demography

* `empiricalB_chr10__expansion_1.004_9.3__h_0.5__results.npz`: ...