diff --git a/docs/effect-size.md b/docs/effect-size.md index 909f4f4..b21cdf8 100644 --- a/docs/effect-size.md +++ b/docs/effect-size.md @@ -207,7 +207,7 @@ The details of sites in tree sequences can be found [here](tskit:sec_site_table_ (trait_frequency_dependence)= -## Frequency dependence +## Frequency Dependence Tstrait supports frequency dependence simulation. It has been shown that rare variants have increased effect sizes compared with common variants @@ -220,7 +220,7 @@ In the frequency dependence model, the following value is multiplied to the effe ```{math} :label: eq:freq-dep -[2p(1-p)^\alpha] +\Big[\sqrt{2p(1-p)}\Big]^\alpha ``` In the above expression, $p$ is the frequency of the causal allele, and @@ -235,13 +235,6 @@ ignore the `alpha` parameter if you are not interested in implementing the frequency dependent model. ::: -The frequency dependence architecture is still an ongoing research topic. While the -frequency dependence model can be used for any trait models in tstrait, it is -suggested that you use the trait model with mean 0 and `alpha` to be -1/2 to conduct -simulations that are widely used in -simulation-based research projects (See -[Speed et al. (2017)](https://doi.org/10.1038/ng.3865) for details). - In the below example, we will be demonstrating how `alpha` influences the simulated effect sizes by using a simulated tree sequence with 10,000 individuals. diff --git a/docs/genetic.md b/docs/genetic.md index a78043f..c510d20 100644 --- a/docs/genetic.md +++ b/docs/genetic.md @@ -29,7 +29,6 @@ After this genetic value page, you will be able to: - Understand how to generate genetic value in tstrait - Understand how to use the user's defined effect sizes to generate genetic values -- Understand the details of frequency dependence model that is supported in tstrait # Algorithm Overview diff --git a/tstrait/genetic_value.py b/tstrait/genetic_value.py index bc90e09..3d8ea57 100644 --- a/tstrait/genetic_value.py +++ b/tstrait/genetic_value.py @@ -51,8 +51,6 @@ class _GeneticValue: trait_df : pandas.DataFrame Dataframe that includes causal site ID, causal allele, simulated effect size, and trait ID. - alpha : float - Parameter that determines the relative weight on rarer variants. """ def __init__(self, ts, trait_df):