Outcross Linkage Map Analyses Add-in for JMP® Genomics

[#1]

1. The Outcross Linkage Map Analyses add-in offers three processes to perform linkage analyses on a full-sib family derived from a cross of two outbred parents. The processes are the Linkage Group and Recombination, Linkage Map Order, and Build QTL Genotype Probability Data Set, and all of them run on an interface of JMP, SAS, and R. This add-in uses the OneMap (Margarido et al. 2007, Hereditas 144: 78-79) R package.
2. This add-in has been build to work with R version 3.6.3 or 4.0.0, and OneMap version 2.1.3. Other versions of R and OneMap may not work properly. The updates in the OneMap package (beginning on version 2.1.3) have effects in some R functions (functions names, and some internal routines), and they will cause errors in the Outcross Add-In of JMP Genomics prior to version 10.0. The necessary fixes in JMP Genomics have already taken place to make the Outcross Add-In compatible with versions OneMap 2.1.3 (the latest OneMap version available in CRAN on March 31st, 2020). These fixes will be available in the JMP Genomics release 10.0.
3. A usage note is available at the webpage http://www.jmp.com/support/notes/52/744.html, where users can find a link to the installation instructions.
4. The newer release of JMP Genomics, version 10.0, has new features tailored to improve the capabilities of the software:
   • The Linkage Group and Recombination process has a new option to form linkage groups, the Transitive Grouping method, as well as a new option to set up R software memory usage.
   • The Linkage Map Order process has two new options to order markers, the Map Order Optimization and Accelerated Map Order Optimization. The former uses SAS PROC OPTMODEL, and the latter uses SAS PROC OPTNET, both of which are powerful and fast methods of optimization suitable to handle the ordering of many markers. Also, a new option to shuffle marker order is available, which may be used to improve overall ordering of markers by shuffling nearby markers on a linkage group.

[sbrlsi]

The newer release of JMP Genomics, version 7.1, has new features tailored to improve the capabilities of the software:

• The Linkage Group and Recombination process has a new option to form linkage groups, the Transitive Grouping method, as well as a new option to set up R software memory usage.
• The Linkage Map Order process has two new options to order markers, the Map Order Optimization and Accelerated Map Order Optimization. The former uses SAS PROC OPTMODEL, and the latter uses SAS PROC OPTNET, both of which are powerful and fast methods of optimization suitable to handle the ordering of many markers. Also, a new option to shuffle marker order is available, which may be used to improve overall ordering of markers by shuffling nearby markers on a linkage group.

[sbrlsi]

The updates in the OneMap package (beginning on version 2.1.0) have effects in some R functions (functions names, and some internal routines), and they will cause errors in the Outcross Add-In of JMP Genomics up to version 9.0. The necessary fixes in JMP Genomics have already taken place to make the Outcross Add-In compatible with versions OneMap 2.1.0 and 2.1.1 (the latest OneMap version available in CRAN on April 9^th, 2018). These fixes will be available in the next release of JMP Genomics. Meanwhile, please contact the Technical Support team to inquire assistance with this issue in OneMap version 2.1.0 or later. Alternatively, you can install OneMap version 2.0.4 or earlier from the the archive https://cran.r-project.org/src/contrib/Archive/onemap/. For your conveniecy, OneMap_2.0.4.zip for Windows system is avaliable for download in this webpage.