For each chromosome, MAPMAKER can remember many facts. These include:
MAPMAKER saves these results between sessions, so that you rarely have to repeat the calculations (until you change your raw data set, of course). Among other things, this mechanism is used to save map data for MAPMAKER/QTL.
For example, we will now store the framework and placements we found for chromosome 10. First we set the sequence to indicate the framework order. Using the name we defined earlier, recalling this sequence without much typing is easy.
One concern is that we are again switching chromosomes (from chromosome 12 back to chromosome 10). MAPMAKER's interface is designed to work one chromosome at a time, and we need to tell it explicitly that we are switching. This is a simple matter, as we need only to precede the list of loci with the name of the chromosome, separated by a colon.
The "framework" command is then used to declare the likely framework order and map of this linkage group. This command computes and then stores this map in your data set, which will be read into MAPMAKER/QTL upon loading. For more details on what MAPMAKER/QTL might do with this information, consult the MAPMAKER/QTL manual.
86> sequence chrom10: best sequence #30= chrom10: best87> framework chrom10 setting framework for chromosome chrom10... ===============================================================================<> chrom10 framework:
Markers Distance 222 M153 7.6 cM 197 M024 3.7 cM 212 M139 1.1 cM 277 A114 6.0 cM 109 M067 3.4 cM 63 D030 16.6 cM 56 L062 2.4 cM 122 M003 6.0 cM 263 A037 2.3 cM 123 M007 2.3 cM 164 M172 3.5 cM 301 T032 4.7 cM 278 A063 8.9 cM 159 M175 ---------- 68.2 cM 14 markers log-likelihood= -102.55 ===============================================================================
Once a framework is set, we can compute and store the map position (relative to the framework ) of any other markers assigned to this chromosome. For this step, we use MAPMAKER's "place" command.
Again, because we don't like to type, we will use a "sequence" shortcut to indicate that we wish to place all assigned markers on this chromosome (MAPMAKER is smart enough not to place markers already in the framework).
The "place" command's output is very similar to that of the order command, described earlier. Briefly, you see:
Section 1: The log-likelihood threshold used by MAPMAKER (2.0 is the default)
Section 2: The map of the framework, not including any of the placed markers.
Section 3: A summary of the placement results and a cartoon of the possible map positions of each marker.
Section 4: The maximum likelihood map(s) resulting when the placed markers are inserted (individually) into their most likely positions. Only the nearby region of the map may be printed, simply to save space.
More detailed information on the "place" command is presented in the Reference section of this manual.
Lastly, we graphically draw these results in a PostScript file using MAPMAKER's "draw chromosome" command. The resulting graphic image is shown on the following page. How you might display or print these graphics is a topic covered in the Installation Guide.
88> sequence assigned sequence #31= chrom10: assigned89> place Placing markers at log-likelihood threshold 2.00... =============================================================================== 1 marker to place on chromosome chrom10...
Framework Map: Markers Distance 222 M153 7.6 cM 197 M024 3.7 cM 212 M139 1.1 cM 277 A114 6.0 cM 109 M067 3.4 cM 63 D030 16.6 cM 56 L062 2.4 cM 122 M003 6.0 cM 263 A037 2.3 cM 123 M007 2.3 cM 164 M172 3.5 cM 301 T032 4.7 cM 278 A063 8.9 cM 159 M175 ---------- 68.2 cM 14 markers log-likelihood= -102.55 Placing Markers: 81 T031 - placed off end of framework, likelihood>5.00 Placements: 222 197 212 277 109 63 56 122 263 123 164 301 278 159 :--8-:--4-:--1-:--6-:--3-:-17-:--2-:--6-:--2-:--2-:--3-:--5-:--9-: 81 2 **.:..*.:....:....:....:....:....:....:....:....:....:....:....:....:... =============================================================================== Best placement of T031: Markers Distance (81) T031 1.2 cM 222 M153 7.6 cM 197 M024 3.7 cM 212 M139 ---------- 12.4 cM 4 markers log-likelihood= -34.53 ===============================================================================
90> draw chromosome Drawing chromosome chrom10 in PostScript file 'chrom10.ps'... ok
Here we see the graphic image produced by MAPMAKER. The framework map is drawn vertically, to scale, with the framework markers in bold type. In regular type we would see markers placed relative to the framework (those italicized cannot be placed in a single unique interval). When showing the distances for placed markers, or small distances (when the number would not fit between the tick marks), MAPMAKER draws the distance next to the markers.
While we have tried to cover many of the MAPMAKER features you will need to analyze typical data sets, there are many other features you may find useful. In fact, this tutorial really only serves as an introduction to the many features available inside MAPMAKER. As you become more familiar with MAPMAKER, we strongly urge you to read through the reference section of this manual, or (equivalently) make use of the on-line "help" command.
Finally, we exit MAPMAKER using the "quit" command. We can now print out our transcript file, "sample.out" to review the results of our work. Because MAPMAKER saves the results of most of its analyses, it is a simple and quick matter to again start up MAPMAKER on these data to quickly explore any small question which comes up.
91> quit saving map data in file 'mouse.maps'... ok saving three-point data in file 'mouse.3pt'... ok