The Linkage Map Order process determines the probable order of genetic markers within linkage groups based on recombination frequencies and calculates the genetic distances between markers to produce a linkage map. Marker ordering is done only within linkage groups.
Multidimensional Scaling is used to find a one-dimensional ordering that best represents the structure found in the matrix of recombination frequencies. A residual plot of the MDS fit can help determine and flag outlier markers that do not fit well in the ordering.
One Input Data Set is required. This data set should be the output data set from the Recombination and Linkage Groups process. It must contain a symmetric matrix of pairwise recombination rates between markers and a variable whose values determine the linkage group to which each marker belongs.
The qtlbc_recombinations.sas7bdat data set, shown below, was generated using the Recombination and Linkage Groups process.
A second, optional, data set is the order data set. This data set contains information about the order of markers that should be used to shape the recombination matrix in the input data set into genetic distances. Each row in this data set should correspond to a row in the symmetric recombination matrix. The qtlbcsample_anno.sas7bdat data set is shown below.
Both the qtlbc_recombinations.sas7bdat and the qtlbcsample_anno.sas7bdat data sets are located in the Sample Data\QtlMapping directory included with JMP Genomics.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.
The output generated by this process is summarized in a Tabbed report. Refer to the Linkage Map Order output documentation for detailed descriptions and guides to interpreting your results.