Manipulating Pleiotropy for MultiTrait Simulation

[B-Abbasi]

AlphaSimR is simulating traits as Pleiotropic where some QTLS are effecting multiple traits, while others are only effecting a single trait.
Can we control this Pleitropy in AlphaSimR to simulate different scenarios of Pleiotropy i.e Non-pleiotropy or all QTLs effecting all traits ?

[gregorgorjanc]

You can control this by specifying uncorrelated traits - see example at https://github.com/HighlanderLab/jbancic_alphasimr_plants/blob/main/04_Features/multipleTraits.R

Or you can import effects (which you simulate according to your interest) - see example at https://github.com/HighlanderLab/jbancic_alphasimr_plants/blob/main/04_Features/importExternalHaplo.R

[B-Abbasi]

Thanks for sharing both options.