Preface to SOLAR Version 6

SOLAR Version 6 introduces EVD (Eigenvalue Decomposition) a method for greatly improving the speed of model maximization, the central operation of all analysis performed by SOLAR. Beta version 6.3.0 uses only a simplified version of EVD called EVD1 which applies only to univariate models and does not yet achieve the full speedup possible. Nevertheless, we have seen performance improvements up to 80 times with actual production data (though the very large pedigree set models we most often use improve about 3 to 4 fold). EVD is not used for all models, only when option modeltype evd is selected or certain new commands are used.

Following on from earlier SNP association analysis techniques QTN and QTLD introduced in earlier versions of SOLAR, a new technique called Measured Genotype Association Analysis is introduced with the new command mgassoc . By default, mgassoc sets up and uses EVD1 for the greatest possible performance. You need only specify the basic model trait and covariates and mgassoc takes care of the rest. When EVD2 or faster techniques are completed, they will be incorporated in mgassoc if possible.

An often requested convenience feature has been added. SOLAR now has command line editing, in which previous solar commands can be recalled with the up and down arrow keys, and the cursor can be repositioned within the current command with the right and left arrow keys. This feature is made possible by the free software program rlwrap by Hans Lub which is included in this distribution. The entire distribution is included along with the pre-installed and scripted program. For help with installation issues on your system, should any arise, or for more information about rlwrap, see the system-specific README file for your system, such as README.linux for linux systems.

As usual, there are many additional improvements which may be viewed with the change-notes command or seen in the Appendix 4 Change Notes. Version 5 was an internal experimental version exploring other less successful methods for improving maximization performance.

Preface to SOLAR Version 4

SOLAR Version 4 introduces multivariate analysis of models with up to 20 quantitative and discrete traits, including mixed quantitative and discrete traits. There is nothing special you need to do for multivariate models except specify all the required traits. For example:

            solar> trait q1 q2 q3 d4

SOLAR handles all the other details. You can simply use all the other commands as you would have done otherwise. (See Chapter 3 for a basic tutorial.) Note however that that the -screen option for polygenic is not allowed for multiple traits, as we believe covariates should be screened for univariate models. For convenience, all LOD scores computed by SOLAR are (by default) "1 df effective" LOD scores which are comparable to those for univariate models. If you wish to see exactly how a LOD score was calculated give the command lod -v when a linkage model is loaded such as after running multipoint. The lodp (lod preferences) command can be used to change how LODs are computed. Further discussion of multivariate analysis is in Chapter 9.

Another important addition to Version 4 is the define command, which can be used to define any variable expression for use as a trait or covariate. A useful inverse normal transformation is supplied for use in the define command, and can also be applied to data in any file using the inormal command.

Association analysis for SNPs can be done using the qtld command after preparing the SNP data using the snp qtld command. Other useful analyses can be performed by other options of the snp command and the snphap command.

For a complete list of changes, see the Change Notes.