We begin this session by performing a classical "two-point" , or pairwise, linkage analysis of our data set. While we generally do not use two-point analysis for ordering markers, we usually do find two-point analysis helpful for identifying linkage groups of markers in preliminary analyses. To then order markers within a group, we use other more powerful techniques.
First, we need to tell MAPMAKER which loci we wish to consider in our two-point analysis. We do this using MAPMAKER's "sequence" command. When you type something like:
sequence locus1 locus2 locus3 ...MAPMAKER is told which loci (and, in some cases, which orders of those loci) any following analysis commands should consider (for ex: locus1, locus2, locus3, etc.). Since almost all of MAPMAKER's analysis functions use the "current sequence" to indicate which loci they should consider, you will find that the "sequence" command must be entered before performing almost any analysis function. The sequence of loci in use remains unchanged until you again type the "sequence" command to change it.
In this two point analysis we want to examine all 12 of the loci in our sample data set. Thus, we now type into MAPMAKER:
sequence 1 2 3 4 5 6 7 8 9 10 11 12Note that for two-point analysis, the order in which the loci are listed is unimportant.
We then type MAPMAKER's "group" command, instructing the program to divide the markers in the sequence into linkage groups. To determine whether any two markers are linked, MAPMAKER calculates the maximum-likelihood distance and corresponding LOD score between the two markers: If the LOD score is greater than some threshold, and if the distance is less than some other threshold, then the markers will be considered linked. By default, the LOD threshold is 3.0, and the distance threshold is 80 Haldane cM.
For the purpose of finding linkage groups, MAPMAKER considers linkage transitive. That is, if marker A is linked to marker B, and if B is linked to C, then A, B, and C will be included in the same linkage group.
As you see, MAPMAKER has divided our data set into two linkage groups, which it names "group1" and "group2". Moreover, there are no unlinked markers in this data set.
Note to users of previous versions of MAPMAKER: It is no longer necessary to use the "two point" command first: MAPMAKER computes two-point data automatically as needed. See the reference manual for details
3> sequence 1 2 3 4 5 6 7 8 9 10 11 12 sequence #1= 1 2 3 4 5 6 7 8 9 10 11 124> group Linkage Groups at min LOD 3.00, max Distance 50.0
group1= 1 2 3 5 7 ------- group2= 4 6 8 9 10 11 12