Variance components models for gene--environment interaction in
twin and sib-pair linkage analysis analysis
Mx scripts |
These Mx scripts are intended to facilitate gene-environment
interaction in twin and sib-pair analysis, specifically when using
continuous moderator variables, as discussed in these two
manuscripts. Also, a special program for plotting variance components as a
function of a moderator variable can be downloaded, gxe-visual. Please reference the articles if you use the
scripts in a publication.
If you have technical problems running these scripts after reading the
associated manuscripts and studying the scripts themselves, please let
me know. The more complex models will often require good starting
values and multiple attempts at convergence. All scripts were developed using the 1.47c Linux version of Mx.
File : gxe-basic.mx
Notes : Datafile must be in the format
ID ZYG T1 T2 M1 M2
Fix parameters T, U, V and B to test for moderated effects
on A, C, E and M respectively.
File : gxe-nl.mx
Notes : As above, but with extra parameters X, Y
and Z representing quadratic interaction terms. Use multiple
start values to ensure a global minimum has been found.
File : gxe-2mod.mx
Notes : Two (linear) moderating variables. Data format
ID ZYG T1 T2 MA1 MA2 MB1 MB2
where MA is the first moderator and MB is the second
moderator (1,2 refers to twin 1, twin 2)
File : gxe-rge.mx and gxe-rge2.mx
Notes : Data format for must be
ZYG T1 T2 M1 M2 M1 M2
i.e. where the same moderator variable is actually entered twice. The
parameters T and U are the interaction parameters for the common and
unique paths. The first script represents the model as described
in the Twin Research article and only allows for moderation of the
additive genetic component. The second script gxe-rge2.mx
applies the same model to the C and E components and should be used in
preference to the first.
File : gxe-qual.mx
Scalar and qualitative GxE
Notes : Data format as for gxe-basic.mx. The A parameter
is the first, unmoderated polygenic component. The T and O
parameters are the second moderated polygenic component.
File : qtl-qxm.mx
Notes : Data format must be
ID ZYG T1 T2 M1 M2 Z0 Z1 Z2
where Z0, Z1 and Z2 are the estimated IBD probabilities at the test
locus. The parameter Q estimates QTL variance; C and E estimate shared
and nonshared residual components. P estimates moderated QTL effects;
U and V represent moderated shared and nonshared residual effects.
File : qtl-exm.mx
Notes : Data format must be
T1 T2 Z0 Z1 Z2 R D1 D2
where Z0, Z1 and Z2 are IBD probabilities, R is the imputed
pair=specific correlation and D1 and D2 are simply `dummy'
columns full of 0's (zeros).
File : qtl-exm.sh
Notes : This file is an excerpt from a script
to create the imputed pair-specific correlation dataset
based on prior estimates of moderated parameters. It is
only intended as an illustrative example -- it would need
to be changed somewhat for different datasets.
A MS Windows 95/98/2000/NT program to
help visualise continuously moderated variance components, with documentation
Mx is the model-fitting package used to implement the DF model.
It can be freely downloaded for various platforms.
GxE Visualisation tool (gxe-visual)
Purcell S (2002). Variance components models for
gene-environment interaction in twin analysis. Twin Research, 5(6), 554-571.
Purcell S & Sham PC (2002). Variance components models
for gene-environment interaction in quantitative trait locus linkage
analysis. Twin Research, 5(6), 572 - 576.
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