ASReml has very comprehensive facilities for estimating functions of variance components. This is done through a ‘.pin file’, which is a text file—separate from the original job file—containing commands to combine the variance components reported in the .asr file. ASReml will automatically calculate the standard error for each function of variance components used in the .pin file.
There are three types of functions supported in a .pin file:
- Linear combinations (F): sums of variance components to create phenotypic variances, for example.
- Ratios (H): to calculate the ratio of two variance components as in heritabilities.
- Correlations (R): to calculate, well, the correlation between two traits.
A .pin file uses the position of the variance components in the .asr file to denote the operations. Thus, let’s assume that the .asr file presents the following results:
Source Model terms Gamma Component Comp/SE % C tree 210 210 0.922524 1.02382 3.01 0 P Variance 228 226 1.00000 1.10980 5.13 0 P
tree (representing additive variance) is in the first position and Variance (the residuals) is in the second position. A .pin file to calculate heritability and its standard error would look like:
F pheno 1 + 2 H herit 1 3
This tells ASReml to sum the first and second variance components (additive and residual variances) and store it in a variable called ‘pheno’, which is the third variance component now. Then ASReml calculates heritability as the ratio of the first variance component (additive variance) and the third (phenotypic variance). Piece of cake!
One normally creates a .pin file with the same names as the .as file. For example, if the job file is called treemodel.as, the .pin file is called treemodel.pin.
To run the .pin file one needs to first run the .as file as in
asreml treemodel and achieve proper convergence for the run. Then one runs the pin file as
asreml -p treemodel, which assumes that there is a treemodel.pin file. If you have named the .pin file differently, then one needs to specify the file name and extension as in
asreml -p anothername.pin.
More coming soon.