Comments (7)
Suggestions in #45
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The dominance model in AlphaSim https://acsess.onlinelibrary.wiley.com/doi/10.3835/plantgenome2016.02.0013 would be a good starting point of the model
from tstrait.
@daikitag we have completely rehauled dominance approach - happy to talk more - this is current implementation https://cran.r-project.org/web/packages/AlphaSimR/vignettes/traits.pdf but that doc doesn't show all the details
from tstrait.
But the basic logic from your initial post is correct. The challenge is how to sample domEffect compared to addEffect - there are some subtle points there with respect to inbreeding depression and heterosis.
from tstrait.
To add - this is similar to other posts - one thing is sampling effects, another is applying them. If you focus on the application of some dominance effects then a user can provide the values or you can provide functionality to sample such effects.
from tstrait.
@gregorgorjanc Thank you very much for your prompt reply. I actually thoroughly read through the codes and architectures of AlphaSimR to learn about quantitative trait simulation before I began this research project, and I tried creating tstrait, such that it can do a similar thing as AlphaSimR to tree sequences.
I found "AlphaSimR uses a digenic dominance model for all ploidy levels due to its use of scaled dominance genotype dosages. This model was chosen because it provides consistency in user interface and internal coding regardless of ploidy level and it provides as a reasonable approximation for partial dominance in highly polygenic traits." to be very interesting to read, as the current codes only support dominance in diploid setting. If you do not mind, would it be possible for you to let me know how you have implemented it, or point out to the codes in AlphaSimR that does it? I'm not sure about how we can implement dominance for polyploids, and I really appreciate your help.
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@daikitag happy to share
In https://cran.r-project.org/web/packages/AlphaSimR/vignettes/traits.pdf you will see section on Genotype dosage scaling and then Additive Effects and Dominance effects
For Genotype dosage scaling the table 1 in that PDF and eq 2 and 3 should be clear I think - let me know if not.
Then we apply the additive and dominance effects to scaled dosages eq 4 and 5, see table 2 example
Codewise see https://github.com/gaynorr/AlphaSimR/blob/695aef000a50061fcef36aad2d85f92b3db2aab5/src/getGv.cpp#L150C24-L150C29
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Related Issues (20)
- Incorrect variance with multiple causal sites HOT 18
- Add statistical tests against existing simulator HOT 15
- Move causal state selection to ``sim_trait`` and make ``sim_genetic`` deterministic (and rename) HOT 7
- Change return type from Pandas dataframe to Xarray dataset? HOT 3
- Change names of fields in return type of sim_phenotype HOT 3
- Change "causal_state" to "causal_allele"? HOT 1
- Review # pragma: no cover usage HOT 1
- Validate against simplePHENOTYPES HOT 1
- Update signatures of sim_phenotype and sim_env HOT 1
- Specify particular causal sites HOT 5
- Quickstart documentation HOT 1
- Option to add -\beta to non-causal nodes HOT 1
- Specifying mean and variance of simulated phenotypes HOT 4
- Degrees of freedom in standard deviation computation HOT 3
- Numba version HOT 2
- Normalize genetic values
- Version 0.1.0 release HOT 11
- New model for trait simulation HOT 1
- Error in rng.choice HOT 6
- Document how ploidy works HOT 3
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