Linkage Phase Data Set

Use this field to specify the full path and name to the Linkage Phase SAS data set.

This data set must contain the elements of the lower triangle matrix of pairwise recombination fraction between markers and the elements of the lower triangle matrix of pairwise LOD values. This data set must contain the variables (columns) listed in the table below:

Required Variable	Description:
Marker1	This variable must contain values that match the values in the Marker ID Variable in the Input SAS Data Set.
Marker2	This variable must contain values that match the values in the Marker ID Variable in the Input SAS Data Set.
rf1 rf2 rf3 rf4	These four variables contain recombination fractions that correspond to the four linkage phase combinations: cis-cis, cis-trans, trans-cis, and trans-trans.
LOD1 LOD2 LOD3 LOD4	These four variables contain LOD values correspond to the four linkage phase combinations: cis-cis, cis-trans, trans-cis, and trans-trans.

To Specify the Linkage Phase Data Set:

The method used for this specification can vary depending on whether JMP is connected to SAS on your local machine or connected to SAS on a server. You should refer to the Specifying Folders, Files, and Data Sets documentation for detailed information.

To View the Contents of the Specified Data Set:

Click Open.