MAPMAKER/EXP Tutorial/Reference Manual 3.0

Verifying a Map Order

There are some obvious caveats with the "order" analysis which are faced by any such "greedy" algorithm (that is, one which adds markers sequentially, building off the previous result with each iteration). If MAPMAKER makes a mistake early on, then all following results may be incorrect. In practice, this is an addressable issue: (1) One reason that MAPMAKER uses a semi-random starting point and addition order is that you should be able to run the "orders" command repeatedly to verify that you get consistent results; (2) MAPMAKER's error detection algorithm, described below, can be used to limit the possible ill-effects of small data errors; and (3) MAPMAKER provides a variety of simple ways of testing the results found by the "order" command.

One powerful command for accomplishing this test is called "ripple". Essentially, given a known (or assumed) map order, "ripple" instructs MAPMAKER to permute the order of neighboring markers, and to compare the likelihoods of the resulting maps. Any order which has a log-likelihood within some threshold amount of the assumed order's likelihood will be displayed as a viable alternative. Like the "orders" command, "ripple" knows how to use three-point analysis to speed its search, although in the end it uses the power of multipoint analysis with all flanking markers to finally compare likelihoods of the consistent orders.

To do this, we first use MAPMAKER's "sequence" command to select the final order we discovered on the previous page, using the name we just defined.

Next, we simply type the "ripple" command. By default, this command will permute 5 neighboring loci at a time and flag all alternative orders within a log-likelihood of 2.0 (that is, within 100:1 or better odds) of that of our known order.

As you can see, MAPMAKER lists the sets of neighboring loci it is permuting as it works. Here, MAPMAKER has reported no alternative orders worth considering. Thus, we have little reason to suspect MAPMAKER's "order" results. 

65> sequence best 
sequence #24= chrom10: M153 M024 M139 A114 M067 D030 L062 M003 A037 M007 M172 T032 A063 M175


66> ripple 
===============================================================================
Map To Test:                
  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
===============================================================================<>
Window-size: 5  Log-likelihood Threshold: 2.00
Comparing maps with ALL flanking markers...

compare    {M153 M024 M139 A114 M067}... ok
compare ...{M024 M139 A114 M067 D030}... ok
compare ...{M139 A114 M067 D030 L062}... ok
compare ...{A114 M067 D030 L062 M003}... ok
compare ...{M067 D030 L062 M003 A037}... ok
compare ...{D030 L062 M003 A037 M007}... ok
compare ...{L062 M003 A037 M007 M172}... ok
compare ...{M003 A037 M007 M172 T032}... ok
compare ...{A037 M007 M172 T032 A063}... ok
compare ...{M007 M172 T032 A063 M175}    ok
===============================================================================<>
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