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9.2 Sample multivar parameter file

The pedigree file for PolyEM programs is similar to that for other Morgan programs. The first three entries in each line consist of the individual's name, father's name and mother's name. Integers starting with the fourth column (usually gender) can be fixed effects (gender, age class, etc.) or discrete phenotypes.

Following the integers we have additional real numbers for quantitative trait measurements. Missing values are recorded as having integer part `999', such as 999.5 in the following example.

Here is part of the pedigree file `polyem_90_ped'.

 
 input pedigree size 90
 input pedigree record names 3 integers 3 reals 2
****************************************
     1     0     0     1     1     0    0.0246   -1.0125
     2     0     0     2     1     0   -0.5978    1.5963
     3     0     0     1     1     0   -0.8124    0.5662
     4     0     0     2     1     0    0.4334    1.7721
     5     1     2     1     1     0    0.1802   -1.4672
     6     1     2     1     1     0   -1.7557    0.8091
     7     3     4     2     1     0    999.5     999.5
     8     3     4     2     1     0    1.9128    0.9780
     9     0     0     2     1     0    0.9530    2.3473
     ...       

Let's go through an example parameter file for multivar line by line. Note in this example, the starting values are chosen to be close to the final values obtained from an earlier run.

 
input pedigree file "polyem_90_ped"

This is the name of the pedigree data file. Note that it can be overridden by command line options, see Command syntax.

 
select trait 1
start trait 1 mean  0.06515

The first trait is the first real number in the pedigree file, with starting mean value 0.06515.

 
select trait 2 effects 1 2
start trait 2 mean  1.80671
start trait 2  effect 1  -0.76589  0.58353
start trait 2  effect 2  -0.99161 -0.55306  1.15920

The second trait is the second column with starting mean 1.80671. Note that trait 2 is specified in its own `select trait' statement.

There are two fixed effects to be modeled for the second trait, the first and second integers (column 4 and 5, note that we start counting from column 4). The first fixed effect has two levels with starting values -0.76589 and 0.58353. The second effect has three levels with corresponding starting values specified in the `start trait' statement.

Those starting values are deviations from the global mean and they are normalized so that the weighted (by the number of individuals in that level) sum is zero to achieve identifiability.

For the variance component part of the trait model, we specify

 
start residual variance     1.10   0.65
start additive variance     0.037  0.0288

These are the initial values for additive and residual variances of the two traits.

 
start residual covariance  -0.09 
start additive covariance  -0.0017

These are the initial values for additive and residual covariances of the traits.

 
fit environmental model            # for multivar

This statement asks multivar to fit a purely environmental model, with no genetic variance. This null hypothesis model is produced in additional to the genetic/environmental model.

 
limit EM iterations 200
output spacing 20 EM iterations

Those options specify the number of EM iterations and how often the EM estimates are printed out.


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