paretobestprint

`paretobestprint`

Concisely describes the best map in the current Pareto frontier.

Synopsis:

The paretobestprint command is invoked as:

paretobestprint Lambda

The paretobestprint command prints a concise description of the best map in the current Pareto frontier. The current Pareto frontier is first extracted from the existing maps in the heap (for each different number of breakpoints, the map which has the maximum likelihood w.r.t. the biological data is selected). Then, the best map is chosen which maximizes the extended likelihood criterion. The traditional $\log_{10}$ -likelihood of the map is printed followed by the order of all the markers (by name), and for each dataset.

Arguments:

Lambda : it corresponds to the expected number of breakpoints between the true order and the reference order. if unknown, it should be set to 1 or to the minimum number of obligate breakpoints (the number of segments minus one in the order dataset) if greater than one.

Returns:

the identifier of the best map in the frontier.

Example:

CG> dsload Data/rh1_true.cg
{1 haploid RH 110 93 /home/tschiex/Dev/carthagene/test/Data/rh1_true.cg}
CG> dsload Data/order1_ref.cg
{2 order 110 /home/tschiex/Dev/carthagene/test/Data/order1_ref.cg}
CG> dsmergor 1 2
{3 merged by order 110 93}
#build a Pareto frontier from scratch
CG> paretolkh 10 1 0
...
#show the best map in the frontier
CG> paretobestprint 1

Pareto frontier approximation (coverage: 39 / 39 = 100.00 %):
Ranges: Log10-likelihood [-1012.378,-957.848] / BP [3,41] = 1.4350
Id:  38 BP:  41 Log10-like:  -957.848 Log10-like+bp: -1095.795
Id:  37 BP:  40 Log10-like:  -957.848 Log10-like+bp: -1092.218
Id:  36 BP:  39 Log10-like:  -958.169 Log10-like+bp: -1088.958           do...
Id:  35 BP:  38 Log10-like:  -957.848 Log10-like+bp: -1085.055
Id:  34 BP:  37 Log10-like:  -957.919 Log10-like+bp: -1081.540
Id:  33 BP:  36 Log10-like:  -958.240 Log10-like+bp: -1078.274           do...
Id:  32 BP:  35 Log10-like:  -958.240 Log10-like+bp: -1074.685
Id:  31 BP:  34 Log10-like:  -958.541 Log10-like+bp: -1071.396
Id:  30 BP:  33 Log10-like:  -958.552 Log10-like+bp: -1067.816
Id:  29 BP:  32 Log10-like:  -962.633 Log10-like+bp: -1068.306           do...
Id:  28 BP:  31 Log10-like:  -959.105 Log10-like+bp: -1061.187
Id:  27 BP:  30 Log10-like:  -961.354 Log10-like+bp: -1059.845
Id:  26 BP:  29 Log10-like:  -962.946 Log10-like+bp: -1057.847           do...
Id:  25 BP:  28 Log10-like:  -961.907 Log10-like+bp: -1053.220
Id:  24 BP:  27 Log10-like:  -963.408 Log10-like+bp: -1051.134           do...
Id:  23 BP:  26 Log10-like:  -962.193 Log10-like+bp: -1046.335
Id:  22 BP:  25 Log10-like:  -964.519 Log10-like+bp: -1045.080           do...
Id:  21 BP:  24 Log10-like:  -963.868 Log10-like+bp: -1040.851
Id:  20 BP:  23 Log10-like:  -965.543 Log10-like+bp: -1038.953           do...
Id:  19 BP:  22 Log10-like:  -965.020 Log10-like+bp: -1034.861
Id:  18 BP:  21 Log10-like:  -966.693 Log10-like+bp: -1032.971
Id:  17 BP:  20 Log10-like:  -968.755 Log10-like+bp: -1031.474           do...
Id:  16 BP:  19 Log10-like:  -968.368 Log10-like+bp: -1027.536
Id:  15 BP:  18 Log10-like:  -970.430 Log10-like+bp: -1026.054
Id:  14 BP:  17 Log10-like:  -972.693 Log10-like+bp: -1024.781
Id:  13 BP:  16 Log10-like:  -973.742 Log10-like+bp: -1022.303
Id:  12 BP:  15 Log10-like:  -976.323 Log10-like+bp: -1021.368
Id:  11 BP:  14 Log10-like:  -979.369 Log10-like+bp: -1020.907
Id:  10 BP:  13 Log10-like:  -981.178 Log10-like+bp: -1019.220
Id:   9 BP:  12 Log10-like:  -982.889 Log10-like+bp: -1017.447
Id:   8 BP:  11 Log10-like:  -985.896 Log10-like+bp: -1016.984
Id:   7 BP:  10 Log10-like:  -987.743 Log10-like+bp: -1015.372
Id:   6 BP:   9 Log10-like:  -991.611 Log10-like+bp: -1015.797
Id:   5 BP:   8 Log10-like:  -993.404 Log10-like+bp: -1014.158
Id:   4 BP:   7 Log10-like:  -996.049 Log10-like+bp: -1013.383           **...
Id:   3 BP:   6 Log10-like: -1001.610 Log10-like+bp: -1015.531
Id:   2 BP:   5 Log10-like: -1003.668 Log10-like+bp: -1014.173
Id:   1 BP:   4 Log10-like: -1008.346 Log10-like+bp: -1015.405
Id:   0 BP:   3 Log10-like: -1012.378 Log10-like+bp: -1015.874

Map  4 : log10-likelihood =  -996.05
-------:
 Set : Marker List ...
   1 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni...
   2 : UniSTS158779 UniSTS164109 UniSTS158781 UniSTS158776 UniSTS207126 Uni...
4
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