Behavioral Genetics Models
Lux Whitehaven
Joined: 02/02/2015
ACE Cholesky; Log Transformed Variables
Hello everyone! I just had a quick question, if anyone has the time to help.
I'm running a multivariate ACE Cholesky on three variables, and outputting individual pathways a11, a21, a31, etc for a, c, and e, as well as overall heritability and environmental estimates, h2, c2, e2. However, one of those variables, the third input one, had a skewness and kurtosis level just outside acceptable ranges.
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YiTan
Joined: 10/08/2014
YiTan
Joined: 10/08/2014
A question on sex limitation model
Hi, I was running the sex limitation model script from http://www.vipbg.vcu.edu/HGEN619_2014/twinHet5AceCon.R and I'm quite surprised that although the initial model fitting shows that the standardized af, cf, ef and am, cm, em values differ greatly, mxCompare reveals no significant difference between the initial model and the homogeneity ACE model. Is there any possible explanation for this?
Thanks!
Here's what I got:
> QualAceSum <- summary(QualAceFit)
> QualAceSum$pa
name matrix row col Estimate Std.Error lbound ubound lboundMet uboundMet
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liuqq1989
Joined: 07/09/2015
Adding covariates to sex-lim ACE model
Hi!
I'm new to twin data analysis and would like to get help on how to adjust for covariates in sex-lim ACE model. I tried to modify the script twinHet5AceCon.R by adding Age（continuous variable） and Region（binary variable）as covariates in the mean structure of the genetic model but I keep getting an error： Unknown reference 'meanGf' detected in the entity 'expMeanGf' in model 'MZf'.
I guess I may did something wrong somewhere near "expMeanGfmCo <- mxAlgebra( expression= meanGfm +Betaall %*% meanGfmCo , name="expMeanGfm" ) ".
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JuliaJoplin
Joined: 10/12/2014
Confidence intervals for shared environmental correlation are (-1.00, 1.00)
In a ACE bivariate Cholesky, any ideas why confidence intervals for a shared environmental correlation would be returned as (-1.00, 1.00)? My syntax is included below. The model converged without any errors.
bivACEModel <- mxModel("bivACE",
mxModel("ACE",
# Matrices a, c, and e to store a, c, and e path coefficients
mxMatrix( type="Lower", nrow=nv, ncol=nv, free=TRUE, values=.8, labels=c("a11","a21","a22"), name="a" ),
mxMatrix( type="Lower", nrow=nv, ncol=nv, free=TRUE, values=.8, labels=c("c11","c21","c22"),name="c" ),
JuliaJoplin
Joined: 10/12/2014
Bivariate Cholesky Assumptions and CTCT Correlations
First time poster here. I'm learning generally about SEM and openMX at the same time and I want to run an ACE bivariate Cholesky decomposition with a sample of twins. I'm using the script below to test assumptions of the model and then run the Cholesky. (This is very similar to existing scripts that are posted, I just added some elements to get confidence intervals for the genetic/shared environmental correlation, and also the phenotypic correlation.)
Alessia
Joined: 05/07/2015
eQTL analysis & IBD
Dear all,
I would like to perform an eQTLs analysis with OpenMx using a IBD matrix inferred by using genotype data. The model I would like to evaluate is the ACQE one. Does someone have some scripts I can use/adapt or some hints about how to deal with this?
Thank you very much!
Alessia
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RFrank
Joined: 06/08/2012
Constraining Components Across Gender Results in Significant Loss of Model Fit?
I'm running a simple ACE model of a continuous variable in openMX. I'm running both a constrained and sex-limited model to see which provides a better fit, and then running various constrained or sex-limited submodels where a or c are dropped.
Here is what I have noticed -- in a sex-limited submodel where c is dropped, the a and e variance components and confidence intervals are extremely similar across males and females -- AND, extremely similar to the components for a constrained model where c is dropped.
wilco92
Joined: 07/15/2010
Sex-lim Bivariate Cholesky
Does anyone know have a script for running a sex-limited bivariate cholesky within same sex twin pairs?
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Yuan
Joined: 02/13/2015
positive/negative genetic correlation
I have just done the bivariate genetic model and I'm not sure about the accuracy of the results.
1. If Rg=-0.76, does this mean the genetic correlation between two traits is negative?
2. is there any relationship between the positive/negative of phenotypic correlation with that of Rg, Rc, or Re? If the phenotypic correlation between two traits is negative, are the Rg, Rc, and Re negative or any of the three can be positive?
Thank you
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