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Merge large linkage groups found on several biological datasets given as arguments.
The multigroup command is invoked as either:
Given a set of markers that are supposed to be on the same chromosome, the aim of the multigroup command is to detect erroneous markers that appear to be poorly linked to the rest of the markers in at least one dataset among several datasets. These erroneous markers can be removed from the current marker selection before computing the best map.
The multigroup command loads a set of biological dataset found in ListOfDataFileName parameter and returns a list of markers such that each marker belongs to a sufficiently large linkage group (of size greater than or equal to SizeThres parameter) in EVERY biological datasets. Linkage groups are computed by a 2-point analysis with ListOfDistThres and ListOfLODThres parameters which specify for each biological data set the distance (in Morgan or in Ray) and LOD thresholds, as used in the usual CarthaGene group command.
# load two datasets and find markers which appear in linkage groups
# of size greater than 4 in the two datasets
CG> set mrkselection [multigroup 4 {0.5 0.5} {6 6} {Data/panelRH1.id Data/p...
Linkage Groups :
---------------:
LOD threshold=6.00
Distance threshold=50.00:
Group ID : Marker ID List ...
1 : 151
2 : 125
3 : 93
4 : 15
5 : 4 36 60 73 79 104 118 123 138 150 161 160 159 158 157 156 155 1...
6 : 1 10 3 2
Linkage Groups :
---------------:
LOD threshold=6.00
Distance threshold=50.00:
Group ID : Marker ID List ...
1 : 151
2 : 149
3 : 123
4 : 122 129 130 131 127 128 126 125 124 137 140 145 146 144 143 142...
5 : 121
6 : 119 120
7 : 118
8 : 116
9 : 115 117
10 : 110 114 113 112 111
11 : 102
12 : 93
13 : 80 81 85 92 100 106 103 105 104 101 99 97 96 95 94 91 98 90 89 ...
14 : 79
15 : 74 78 77 76 75
16 : 73
17 : 59 63 69 72 71 68 67 66 65 64 62 61 60 70
18 : 58
19 : 46 55 57 56 54 53 52 51 50 49 48 47
20 : 41 45 44 43 42
21 : 40
22 : 35 36 37 39 38
23 : 30 31
24 : 11 15 20 28 33 32 29 24 27 26 25 23 22 21 19 18 17 14 16 13 12 34
25 : 10
26 : 4 9 8 7 6 5
27 : 1 3 2
122 129 130 131 127 128 126 124 137 140 145 146 144 143 142 141 139 138 136...
CG>
# merge the two panels
CG> dsmergor 1 2
{3 merged by order 161 273}
CG>
# set the current selection of markers
CG> mrkselset $mrkselection
CG>
# remove double markers
CG> mrkdouble
Possible double markers:
4 = 5 [45.9]
CG> mrkmerges
Markers 4 and 5 merged in 4.
CG>
# find a good map
CG> lkhn 1 -1
[-2693.73]
Best map with log10-likelihood = -2693.73
TSP: optimum= 2612.586000 lowerbound= 2610.091410 gap= 0.095575% totaltime=...
Map -1 : log10-likelihood = -2693.73
-------:
Set : Marker List ...
1 : 9 8 7 6 4 11 13 12 14 17 16 18 19 20 21 22 23 24 27 25 26 28 29 32 3...
2 : 9 8 7 6 4 11 13 12 14 17 16 18 19 20 21 22 23 24 27 25 26 28 29 32 3...
CG> bestprintd
Map 0 : log10-likelihood = -2693.73, log-e-likelihood = -6202.55
-------:
Data Set Number 1 :
Markers Distance Cumulative Theta 2pt
Pos Id name (%%age) LOD
1 9 9 19.1 cR 0.0 cR 17.4 %% 14.9
2 8 8 0.0 cR 19.1 cR 0.0 %% 18.6
3 7 7 24.5 cR 19.1 cR 21.8 %% 12.1
4 6 6 20.5 cR 43.7 cR 18.5 %% 10.0
5 5 5 0.0 cR 64.1 cR 0.0 %% ------
5 4 4 19.9 cR 64.1 cR 18.1 %% 12.3
6 11 11 21.3 cR 84.0 cR 19.2 %% 12.0
7 13 13 17.5 cR 105.3 cR 16.1 %% 10.6
8 12 12 19.3 cR 122.9 cR 17.5 %% 7.5
9 14 14 35.4 cR 142.1 cR 29.8 %% 5.7
10 17 17 3.9 cR 177.6 cR 3.8 %% 15.9
11 16 16 0.0 cR 181.4 cR 0.0 %% 19.3
12 18 18 3.5 cR 181.5 cR 3.4 %% 15.9
13 19 19 0.0 cR 184.9 cR 0.0 %% 17.0
14 20 20 7.0 cR 185.0 cR 6.8 %% 14.6
15 21 21 7.0 cR 192.0 cR 6.8 %% 15.3
16 22 22 8.7 cR 199.0 cR 8.3 %% 13.2
17 23 23 4.4 cR 207.7 cR 4.3 %% 13.7
18 24 24 13.6 cR 212.1 cR 12.7 %% 10.7
19 27 27 11.1 cR 225.7 cR 10.5 %% 12.2
20 25 25 7.2 cR 236.8 cR 6.9 %% 14.7
21 26 26 15.3 cR 244.0 cR 14.2 %% 11.3
22 28 28 7.3 cR 259.3 cR 7.1 %% 14.4
23 29 29 0.0 cR 266.7 cR 0.0 %% 17.0
24 32 32 3.5 cR 266.7 cR 3.4 %% 16.7
25 33 33 3.5 cR 270.1 cR 3.4 %% 16.7
26 34 34 30.0 cR 273.6 cR 26.0 %% 7.2
27 35 35 28.5 cR 303.7 cR 24.8 %% 7.7
28 36 36 12.2 cR 332.2 cR 11.5 %% 12.8
29 37 37 7.8 cR 344.4 cR 7.5 %% 13.8
30 38 38 34.9 cR 352.2 cR 29.4 %% 5.4
31 39 39 33.2 cR 387.0 cR 28.2 %% 3.0
32 44 44 45.5 cR 420.2 cR 36.6 %% 3.7
33 41 41 26.3 cR 465.8 cR 23.1 %% 10.1
34 42 42 6.9 cR 492.1 cR 6.6 %% 15.9
35 43 43 3.3 cR 499.0 cR 3.3 %% 17.9
36 45 45 7.8 cR 502.3 cR 7.5 %% 15.1
37 46 46 16.4 cR 510.1 cR 15.1 %% 12.4
38 49 49 10.2 cR 526.5 cR 9.7 %% 13.3
39 51 51 3.2 cR 536.7 cR 3.2 %% 17.8
40 50 50 0.0 cR 539.9 cR 0.0 %% 21.7
41 47 47 0.0 cR 539.9 cR 0.0 %% 21.7
42 48 48 0.0 cR 540.0 cR 0.0 %% 21.7
43 52 52 0.0 cR 540.0 cR 0.0 %% 21.0
44 53 53 3.2 cR 540.0 cR 3.2 %% 17.1
45 54 54 6.5 cR 543.2 cR 6.3 %% 15.7
46 55 55 38.2 cR 549.7 cR 31.7 %% 7.6
47 56 56 12.3 cR 587.8 cR 11.6 %% 10.6
48 57 57 39.5 cR 600.1 cR 32.7 %% 7.7
49 59 59 51.8 cR 639.7 cR 40.5 %% 6.6
50 60 60 12.6 cR 691.5 cR 11.8 %% 12.0
51 64 64 29.3 cR 704.1 cR 25.4 %% 8.8
52 63 63 22.7 cR 733.4 cR 20.3 %% 12.7
53 61 61 5.9 cR 756.1 cR 5.7 %% 19.4
54 62 62 11.0 cR 762.0 cR 10.5 %% 14.8
55 65 65 13.6 cR 773.0 cR 12.7 %% 13.1
56 66 66 22.9 cR 786.6 cR 20.5 %% 11.5
57 69 69 10.7 cR 809.5 cR 10.2 %% 14.2
58 71 71 6.5 cR 820.3 cR 6.3 %% 15.4
59 72 72 16.4 cR 826.8 cR 15.2 %% 15.5
60 70 70 3.6 cR 843.2 cR 3.5 %% 19.9
61 68 68 37.5 cR 846.8 cR 31.3 %% 6.3
62 67 67 46.6 cR 884.3 cR 37.2 %% 4.1
63 77 77 38.1 cR 930.9 cR 31.7 %% 7.7
64 75 75 0.0 cR 969.0 cR 0.0 %% 22.1
65 76 76 6.1 cR 969.0 cR 5.9 %% 18.5
66 78 78 16.5 cR 975.1 cR 15.2 %% 14.4
67 74 74 43.5 cR 991.6 cR 35.3 %% 8.1
68 80 80 36.1 cR 1035.1 cR 30.3 %% 7.7
69 81 81 14.0 cR 1071.2 cR 13.1 %% 12.4
70 82 82 3.2 cR 1085.2 cR 3.1 %% 19.6
71 83 83 29.6 cR 1088.4 cR 25.6 %% 9.4
72 84 84 20.0 cR 1118.0 cR 18.1 %% 10.9
73 85 85 17.5 cR 1138.0 cR 16.0 %% 12.9
74 86 86 10.5 cR 1155.4 cR 10.0 %% 17.3
75 88 88 35.1 cR 1166.0 cR 29.6 %% 8.7
76 87 87 46.6 cR 1201.1 cR 37.2 %% 4.8
77 98 98 32.9 cR 1247.7 cR 28.0 %% 5.0
78 89 89 19.0 cR 1280.5 cR 17.3 %% 9.6
79 90 90 38.0 cR 1299.6 cR 31.6 %% 9.2
80 91 91 3.4 cR 1337.5 cR 3.4 %% 19.8
81 92 92 27.5 cR 1341.0 cR 24.1 %% 10.7
82 94 94 29.6 cR 1368.5 cR 25.7 %% 9.6
83 95 95 0.0 cR 1398.1 cR 0.0 %% 19.0
84 96 96 20.8 cR 1398.1 cR 18.8 %% 13.3
85 97 97 9.4 cR 1418.9 cR 9.0 %% 17.4
86 99 99 0.0 cR 1428.4 cR 0.0 %% 21.5
87 100 100 3.1 cR 1428.4 cR 3.1 %% 18.9
88 101 101 24.4 cR 1431.5 cR 21.7 %% 11.7
89 104 104 48.3 cR 1455.9 cR 38.3 %% 5.2
90 105 105 43.1 cR 1504.2 cR 35.0 %% 4.8
91 103 103 22.5 cR 1547.3 cR 20.2 %% 9.5
92 106 106 7.6 cR 1569.9 cR 7.3 %% 15.1
93 107 107 3.2 cR 1577.4 cR 3.2 %% 19.1
94 109 109 0.0 cR 1580.6 cR 0.0 %% 21.7
95 108 108 0.0 cR 1580.6 cR 0.0 %% 21.7
96 111 111 3.2 cR 1580.7 cR 3.2 %% 19.1
97 113 113 10.2 cR 1583.9 cR 9.7 %% 14.0
98 112 112 6.6 cR 1594.1 cR 6.4 %% 15.8
99 110 110 3.2 cR 1600.7 cR 3.1 %% 19.5
100 114 114 59.2 cR 1603.8 cR 44.7 %% 5.4
101 122 122 21.8 cR 1663.0 cR 19.6 %% 11.5
102 124 124 25.1 cR 1684.8 cR 22.2 %% 9.6
103 126 126 18.5 cR 1709.9 cR 16.9 %% 8.9
104 127 127 50.3 cR 1728.4 cR 39.5 %% 4.1
105 129 129 19.0 cR 1778.6 cR 17.3 %% 8.9
106 128 128 25.2 cR 1797.6 cR 22.2 %% 7.3
107 130 130 11.2 cR 1822.7 cR 10.6 %% 9.8
108 131 131 36.3 cR 1833.9 cR 30.4 %% 6.5
109 134 134 14.3 cR 1870.2 cR 13.4 %% 12.4
110 133 133 17.0 cR 1884.6 cR 15.6 %% 8.1
111 136 136 25.4 cR 1901.6 cR 22.4 %% 7.5
112 138 138 16.8 cR 1927.0 cR 15.4 %% 12.9
113 141 141 5.1 cR 1943.7 cR 4.9 %% 15.5
114 139 139 12.4 cR 1948.8 cR 11.6 %% 13.9
115 140 140 0.0 cR 1961.1 cR 0.0 %% 22.7
116 142 142 0.0 cR 1961.2 cR 0.0 %% 22.7
117 135 135 0.0 cR 1961.2 cR 0.0 %% 22.7
118 137 137 3.1 cR 1961.2 cR 3.1 %% 20.1
119 132 132 33.2 cR 1964.3 cR 28.3 %% 10.7
120 143 143 8.6 cR 1997.5 cR 8.2 %% 19.2
121 145 145 2.9 cR 2006.1 cR 2.9 %% 20.7
122 144 144 11.9 cR 2009.0 cR 11.2 %% 16.3
123 146 146 6.4 cR 2020.9 cR 6.2 %% 19.7
124 148 148 22.7 cR 2027.3 cR 20.3 %% 13.3
125 152 152 16.6 cR 2050.0 cR 15.3 %% 12.6
126 154 154 9.5 cR 2066.7 cR 9.0 %% 15.7
127 159 159 14.2 cR 2076.1 cR 13.2 %% 16.9
128 160 160 0.0 cR 2090.3 cR 0.0 %% 26.5
129 161 161 13.9 cR 2090.3 cR 13.0 %% 16.8
130 157 157 8.5 cR 2104.3 cR 8.1 %% 18.7
131 158 158 8.3 cR 2112.7 cR 8.0 %% 19.1
132 155 155 14.3 cR 2121.1 cR 13.3 %% 16.9
133 156 156 14.6 cR 2135.3 cR 13.6 %% 17.1
134 153 153 12.9 cR 2149.9 cR 12.1 %% 16.7
135 150 150 18.2 cR 2162.8 cR 16.6 %% 13.5
136 147 147 ---------
2181.0 cR
136 markers, log10-likelihood = -883.33
log-e-likelihood = -2033.94
retention proba. = 0.21
Data Set Number 2 :
Markers Distance Cumulative Theta 2pt
Pos Id name (%%age) LOD
1 9 9 29.8 cR 0.0 cR 25.8 %% 9.0
2 8 8 9.1 cR 29.8 cR 8.7 %% 14.0
3 7 7 24.8 cR 39.0 cR 22.0 %% 11.3
4 6 6 8.2 cR 63.8 cR 7.9 %% 18.9
5 5 5 0.0 cR 72.0 cR 0.0 %% ------
5 4 4 81.6 cR 72.0 cR 55.8 %% 2.7
6 11 11 24.8 cR 153.6 cR 22.0 %% 10.4
7 13 13 11.0 cR 178.4 cR 10.4 %% 17.0
8 12 12 38.2 cR 189.4 cR 31.8 %% 6.3
9 14 14 29.0 cR 227.7 cR 25.2 %% 9.0
10 17 17 11.9 cR 256.7 cR 11.2 %% 20.5
11 16 16 8.5 cR 268.5 cR 8.1 %% 23.3
12 18 18 15.7 cR 277.0 cR 14.5 %% 18.7
13 19 19 10.4 cR 292.7 cR 9.8 %% 20.6
14 20 20 4.9 cR 303.0 cR 4.7 %% 25.3
15 21 21 26.1 cR 307.9 cR 23.0 %% 13.9
16 22 22 0.0 cR 334.0 cR 0.0 %% 22.3
17 23 23 15.5 cR 334.0 cR 14.4 %% 12.3
18 24 24 15.5 cR 349.5 cR 14.4 %% 12.4
19 27 27 14.5 cR 365.0 cR 13.5 %% 15.3
20 25 25 2.7 cR 379.5 cR 2.6 %% 20.4
21 26 26 16.7 cR 382.1 cR 15.4 %% 14.4
22 28 28 40.7 cR 398.8 cR 33.5 %% 7.6
23 29 29 18.0 cR 439.5 cR 16.5 %% 11.3
24 32 32 33.1 cR 457.5 cR 28.2 %% 9.8
25 33 33 14.8 cR 490.7 cR 13.8 %% 17.0
26 34 34 56.3 cR 505.5 cR 43.1 %% 7.2
27 35 35 24.3 cR 561.8 cR 21.5 %% 11.3
28 36 36 40.8 cR 586.1 cR 33.5 %% 10.5
29 37 37 73.5 cR 626.9 cR 52.1 %% 4.8
30 38 38 17.8 cR 700.4 cR 16.3 %% 9.2
31 39 39 98.9 cR 718.2 cR 62.8 %% 0.4
32 44 44 26.4 cR 817.1 cR 23.2 %% 9.4
33 41 41 5.2 cR 843.5 cR 5.1 %% 21.0
34 42 42 2.6 cR 848.7 cR 2.5 %% 23.3
35 43 43 5.2 cR 851.3 cR 5.1 %% 21.0
36 45 45 54.8 cR 856.5 cR 42.2 %% 7.2
37 46 46 15.5 cR 911.3 cR 14.3 %% 22.1
38 49 49 15.2 cR 926.8 cR 14.1 %% 22.8
39 51 51 12.3 cR 941.9 cR 11.6 %% 21.1
40 50 50 7.3 cR 954.2 cR 7.1 %% 22.4
41 47 47 10.0 cR 961.5 cR 9.5 %% 20.5
42 48 48 30.8 cR 971.6 cR 26.5 %% 9.3
43 52 52 35.5 cR 1002.4 cR 29.9 %% 8.4
44 53 53 14.1 cR 1037.9 cR 13.2 %% 19.5
45 54 54 22.2 cR 1052.0 cR 19.9 %% 19.8
46 55 55 42.3 cR 1074.2 cR 34.5 %% 13.9
47 56 56 2.4 cR 1116.5 cR 2.3 %% 30.6
48 57 57 62.4 cR 1118.9 cR 46.4 %% 10.0
49 59 59 34.7 cR 1181.3 cR 29.3 %% 15.8
50 60 60 25.7 cR 1216.0 cR 22.7 %% 14.0
51 64 64 25.7 cR 1241.7 cR 22.7 %% 14.0
52 63 63 15.6 cR 1267.5 cR 14.5 %% 24.0
53 61 61 2.8 cR 1283.1 cR 2.8 %% 31.4
54 62 62 27.6 cR 1285.9 cR 24.1 %% 17.1
55 65 65 16.7 cR 1313.5 cR 15.4 %% 21.5
56 66 66 30.2 cR 1330.2 cR 26.1 %% 16.4
57 69 69 9.4 cR 1360.5 cR 9.0 %% 24.5
58 71 71 41.0 cR 1369.9 cR 33.6 %% 10.3
59 72 72 46.9 cR 1410.9 cR 37.4 %% 5.4
60 70 70 37.1 cR 1457.8 cR 31.0 %% 7.6
61 68 68 13.6 cR 1494.9 cR 12.7 %% 17.9
62 67 67 94.3 cR 1508.5 cR 61.1 %% 3.4
63 77 77 18.8 cR 1602.8 cR 17.1 %% 17.1
64 75 75 17.9 cR 1621.6 cR 16.4 %% 16.2
65 76 76 13.8 cR 1639.5 cR 12.9 %% 19.5
66 78 78 16.1 cR 1653.3 cR 14.9 %% 18.5
67 74 74 82.2 cR 1669.4 cR 56.0 %% 5.7
68 80 80 37.1 cR 1751.6 cR 31.0 %% 11.7
69 81 81 19.3 cR 1788.6 cR 17.5 %% 16.9
70 82 82 19.2 cR 1807.9 cR 17.4 %% 19.2
71 83 83 33.6 cR 1827.1 cR 28.5 %% 14.5
72 84 84 26.1 cR 1860.6 cR 22.9 %% 18.3
73 85 85 23.6 cR 1886.7 cR 21.0 %% 19.1
74 86 86 9.6 cR 1910.3 cR 9.2 %% 23.8
75 88 88 16.5 cR 1919.9 cR 15.2 %% 16.1
76 87 87 42.1 cR 1936.4 cR 34.4 %% 7.9
77 98 98 27.3 cR 1978.5 cR 23.9 %% 8.4
78 89 89 10.5 cR 2005.8 cR 10.0 %% 12.7
79 90 90 20.2 cR 2016.3 cR 18.3 %% 16.1
80 91 91 7.7 cR 2036.5 cR 7.4 %% 25.5
81 92 92 11.8 cR 2044.2 cR 11.2 %% 23.4
82 94 94 6.9 cR 2056.0 cR 6.7 %% 26.4
83 95 95 25.0 cR 2063.0 cR 22.1 %% 17.8
84 96 96 28.8 cR 2088.0 cR 25.0 %% 15.8
85 97 97 48.3 cR 2116.8 cR 38.3 %% 10.9
86 99 99 9.6 cR 2165.1 cR 9.2 %% 25.2
87 100 100 6.4 cR 2174.7 cR 6.2 %% 29.6
88 101 101 17.2 cR 2181.1 cR 15.8 %% 24.1
89 104 104 15.6 cR 2198.3 cR 14.4 %% 22.0
90 105 105 6.8 cR 2213.9 cR 6.6 %% 24.7
91 103 103 42.6 cR 2220.7 cR 34.7 %% 11.3
92 106 106 22.4 cR 2263.3 cR 20.1 %% 18.4
93 107 107 22.0 cR 2285.7 cR 19.7 %% 22.1
94 109 109 49.7 cR 2307.7 cR 39.2 %% 10.5
95 108 108 61.7 cR 2357.5 cR 46.0 %% 5.4
96 111 111 12.2 cR 2419.1 cR 11.5 %% 22.8
97 113 113 0.0 cR 2431.4 cR 0.0 %% 34.4
98 112 112 13.1 cR 2431.4 cR 12.3 %% 25.8
99 110 110 31.5 cR 2444.5 cR 27.0 %% 17.0
100 114 114 180.9 cR 2476.0 cR 83.6 %% 0.8
101 122 122 49.7 cR 2656.8 cR 39.1 %% 10.4
102 124 124 7.7 cR 2706.5 cR 7.4 %% 31.1
103 126 126 2.8 cR 2714.2 cR 2.8 %% 33.4
104 127 127 23.6 cR 2717.1 cR 21.0 %% 19.0
105 129 129 11.7 cR 2740.7 cR 11.0 %% 21.8
106 128 128 8.5 cR 2752.3 cR 8.1 %% 23.8
107 130 130 46.8 cR 2760.8 cR 37.3 %% 11.5
108 131 131 12.8 cR 2807.6 cR 12.0 %% 19.5
109 134 134 14.7 cR 2820.4 cR 13.7 %% 16.9
110 133 133 60.8 cR 2835.1 cR 45.6 %% 5.0
111 136 136 39.8 cR 2895.9 cR 32.9 %% 9.5
112 138 138 19.9 cR 2935.8 cR 18.0 %% 15.3
113 141 141 28.4 cR 2955.7 cR 24.7 %% 13.9
114 139 139 4.7 cR 2984.0 cR 4.6 %% 29.8
115 140 140 17.4 cR 2988.7 cR 16.0 %% 20.7
116 142 142 36.8 cR 3006.1 cR 30.8 %% 14.2
117 135 135 17.4 cR 3042.9 cR 16.0 %% 22.8
118 137 137 21.6 cR 3060.4 cR 19.4 %% 22.7
119 132 132 42.1 cR 3082.0 cR 34.4 %% 15.8
120 143 143 25.9 cR 3124.1 cR 22.8 %% 22.1
121 145 145 6.7 cR 3149.9 cR 6.5 %% 30.8
122 144 144 36.2 cR 3156.6 cR 30.4 %% 17.1
123 146 146 31.4 cR 3192.8 cR 26.9 %% 17.4
124 148 148 30.2 cR 3224.2 cR 26.1 %% 14.9
125 152 152 28.9 cR 3254.4 cR 25.1 %% 16.2
126 154 154 29.2 cR 3283.4 cR 25.3 %% 17.6
127 159 159 8.5 cR 3312.5 cR 8.2 %% 28.7
128 160 160 23.4 cR 3321.1 cR 20.9 %% 22.5
129 161 161 32.4 cR 3344.5 cR 27.7 %% 17.9
130 157 157 16.3 cR 3376.9 cR 15.0 %% 22.0
131 158 158 10.9 cR 3393.1 cR 10.3 %% 26.1
132 155 155 15.3 cR 3404.0 cR 14.2 %% 24.1
133 156 156 14.6 cR 3419.3 cR 13.6 %% 25.9
134 153 153 20.9 cR 3433.9 cR 18.9 %% 23.8
135 150 150 87.0 cR 3454.8 cR 58.1 %% 7.1
136 147 147 ---------
3541.8 cR
136 markers, log10-likelihood = -1810.40
log-e-likelihood = -4168.61
retention proba. = 0.14
0
CG>
Thomas Schiex 2009-10-27