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Display the Heap of maps in details.
The CarthaGene heaprintd command is invoked as either one of :
heaprintd provide a output of the heap of maps. The maps are ordered by loglikelihood. The best map is always the last printed. The informations available are the id of a map, the score, and the ordered list of the markers printed by names, ids and positions on the map. This last information is usefull for "merged by order" data sets. Distances and two points informations for consecutives markers are also available. At the end, some statistics are delivered to give the computational cost of the result.
If the data set the maps are computed on, is merged by order, relatives orders for each merged data sets are printed for each maps.
# a very small heap for the example
CG> heapsize 1
CG> dsload Data/bc1.cg
{1 f2 backcross 17 208 /homes/thomas/carthagene/test/Data/bc1.cg}
CG> sem
Map -1 : log10-likelihood = -485.24
-------:
Set : Marker List ...
1 : MS4 MS5 MS13 MS6 MS11 MS17 MS16 MS8 MS7 MS2 MS3 MS9 MS15 MS12 MS20 M...
# we fill the heap with the best map
CG> flips 3 0 0
...
# and look at it
CG> heaprintd
Map 0 : log10-likelihood = -460.57, log-e-likelihood = -1060.49
-------:
Data Set Number 1 :
Markers Distance Cumulative Distance Theta 2pt
Pos Id name Haldane Haldane Kosambi (%%age) LOD
1 1 MS4 3.1 cM 3.1 cM 3.0 cM 3.0 %% 21.1
2 2 MS5 4.0 cM 7.1 cM 3.9 cM 3.9 %% 15.4
3 4 MS6 28.2 cM 35.3 cM 23.0 cM 21.5 %% 5.1
4 5 MS11 8.0 cM 43.3 cM 7.4 cM 7.4 %% 11.9
5 3 MS13 39.8 cM 83.1 cM 30.9 cM 27.5 %% 0.9
6 6 MS17 22.1 cM 105.2 cM 18.7 cM 17.9 %% 6.3
7 7 MS16 33.5 cM 138.7 cM 26.7 cM 24.4 %% 10.3
8 8 MS8 6.3 cM 145.0 cM 5.9 cM 5.9 %% 35.1
9 9 MS7 17.2 cM 162.2 cM 15.0 cM 14.5 %% 21.1
10 10 MS2 0.6 cM 162.8 cM 0.6 cM 0.6 %% 47.6
11 11 MS3 28.9 cM 191.7 cM 23.6 cM 22.0 %% 12.8
12 12 MS9 20.8 cM 212.5 cM 17.7 cM 17.0 %% 13.6
13 13 MS15 3.6 cM 216.1 cM 3.5 cM 3.5 %% 26.5
14 14 MS12 51.8 cM 267.9 cM 38.3 cM 32.2 %% 4.3
15 15 MS20 2.9 cM 270.7 cM 2.8 cM 2.8 %% 34.8
16 16 MS19 345.4 cM 616.1 cM 190.0 cM 50.0 %% -0.0
17 17 MS1 ---------- ----------
616.1 cM 411.0 cM
17 markers, log10-likelihood = -460.57
log-e-likelihood = -1060.49
EM calls:
Set 1 : 67 (60,0)
CPU Time (secs): 0.05
Maps within -3.0: 1
# same thing with maps merged by order
CG> dsload Data/rh1.cg
{2 haploid RH 13 118 /homes/thomas/carthagene/test/Data/rh1.cg}
CG> dsmergor 1 2
{3 merged by order 21 326}
CG> sem
Map -1 : log10-likelihood = -801.56
-------:
Set : Marker List ...
1 : MS4 MS5 MS13 MS6 MS11 MS17 MS16 MS8 MS7 MS2 MS3 MS9 MS15 MS12 MS20 M...
2 : MS4 MS5 MS6 MS8 MS7 MS3 MS9 MS15 ...
CG> flips 3 3.0 1
...
# each map is a pair of map
CG> heaprintd
Map 0 : log10-likelihood = -727.95, log-e-likelihood = -1676.16
-------:
Data Set Number 1 :
Markers Distance Cumulative Distance Theta 2pt
Pos Id name Haldane Haldane Kosambi (%%age) LOD
1 1 MS4 3.1 cM 3.1 cM 3.0 cM 3.0 %% 21.1
2 2 MS5 3.8 cM 6.9 cM 3.7 cM 3.7 %% 15.4
3 4 MS6 26.1 cM 33.0 cM 21.6 cM 20.3 %% 5.1
4 5 MS11 8.6 cM 41.6 cM 8.0 cM 7.9 %% 11.9
5 3 MS13 14.3 cM 56.0 cM 12.7 cM 12.5 %% 9.7
6 7 MS16 19.6 cM 75.6 cM 16.8 cM 16.2 %% 6.3
7 6 MS17 60.6 cM 136.2 cM 43.6 cM 35.1 %% 0.0
8 9 MS7 5.7 cM 141.9 cM 5.4 cM 5.4 %% 29.4
9 12 MS9 1.9 cM 143.8 cM 1.8 cM 1.8 %% 40.8
10 8 MS8 25.8 cM 169.6 cM 21.4 cM 20.1 %% 15.1
11 11 MS3 0.6 cM 170.2 cM 0.6 cM 0.6 %% 47.6
12 10 MS2 62.0 cM 232.2 cM 44.4 cM 35.5 %% 4.3
13 14 MS12 4.3 cM 236.5 cM 4.1 cM 4.1 %% 26.5
14 13 MS15 41.3 cM 277.8 cM 31.8 cM 28.1 %% 6.9
15 16 MS19 2.9 cM 280.7 cM 2.9 cM 2.9 %% 34.8
16 15 MS20 345.4 cM 626.1 cM 190.0 cM 50.0 %% -0.0
17 17 MS1 ---------- ----------
626.1 cM 411.8 cM
17 markers, log10-likelihood = -447.28
log-e-likelihood = -1029.91
Data Set Number 2 :
Markers Distance Cumulative Theta 2pt
Pos Id name (%%age) LOD
1 1 MS4 85.0 cR 85.0 cR 57.3 %% 3.6
2 2 MS5 57.9 cR 143.0 cR 44.0 %% 7.4
3 4 MS6 33.2 cR 176.2 cR 28.2 %% 12.8
8 9 MS7 77.0 cR 253.2 cR 53.7 %% 5.4
9 12 MS9 17.0 cR 270.1 cR 15.6 %% 18.5
10 8 MS8 233.1 cR 503.3 cR 90.3 %% 0.2
11 11 MS3 760.1 cR 1263.4 cR 100.0 %% -0.0
14 13 MS15 760.1 cR 2023.4 cR 100.0 %% -0.0
17 17 MS1 95.5 cR 2118.9 cR 61.5 %% 2.7
18 20 G37 25.3 cR 2144.2 cR 22.4 %% 15.0
19 21 G40 21.5 cR 2165.7 cR 19.3 %% 17.2
20 18 G36 59.8 cR 2225.5 cR 45.0 %% 7.7
21 19 G39 ---------
2225.5 cR
13 markers, log10-likelihood = -280.67
log-e-likelihood = -646.26
retention proba. = 0.24
EM calls:
Set 3 : 876 (0,0)
Set 1 : 877 (855,0)
Set 2 : 877 (858,0)
CPU Time (secs): 1.07
Maps within -3.0: 1
Thomas Schiex 2009-10-27