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sbrlsi

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Jun 20, 2014

Outcross Linkage Map Analyses Add-in for JMP® Genomics

<HTML><HEAD></HEAD><BODY><OL><LI><SPAN style="color: #000000; font-size: 12pt; font-family: arial,helvetica,sans-serif; mso-fareast-font-family: 'Times New Roman';">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.</SPAN></LI><LI><SPAN style="font-family: arial,helvetica,sans-serif; font-size: 12pt;"><SPAN style="color: #000000; mso-fareast-font-family: 'Times New Roman';">A usage note is available at the webpage </SPAN><A href="http://www.jmp.com/support/notes/52/744.html" title="http://www.jmp.com/support/notes/52/744.html" rel="noopener noreferrer"><SPAN style="color: blue; text-decoration: underline; mso-fareast-font-family: 'Times New Roman';">http://www.jmp.com/support/notes/52/744.html</SPAN></A><SPAN style="color: #000000; mso-fareast-font-family: 'Times New Roman';">, where users can find a link to the installation instructions.</SPAN></SPAN></LI><LI><SPAN style="color: #000000; font-size: 12pt; font-family: arial,helvetica,sans-serif; mso-fareast-font-family: 'Times New Roman';">The newer release of JMP Genomics, version 7.1, has new features tailored to improve the capabilities of the software:</SPAN><UL><LI><SPAN style="color: #000000; font-size: 12pt; font-family: arial,helvetica,sans-serif; mso-fareast-font-family: 'Times New Roman';">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. </SPAN></LI><LI><SPAN style="color: #000000; font-size: 12pt; font-family: arial,helvetica,sans-serif; mso-fareast-font-family: 'Times New Roman';">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.</SPAN><SPAN style="color: #000000; font-size: 12pt; line-height: 1.5em;"> </SPAN></LI></UL></LI></OL><P></P><P><LI-IMAGE id="609i8F222977F4718152" width="1365" height="728" alt="6879_RLGOutcross.PNG" align="inline" resized="false" size="medium" sourcetype="new"></LI-IMAGE></P><P><LI-IMAGE id="610i1EDDAE81F72E59FA" width="985" height="709" alt="6880_MOOutcross.PNG" align="inline" resized="false" size="medium" sourcetype="new"></LI-IMAGE></P></BODY></HTML>

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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 9th, 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.