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In CarthaGene, all the two points information (LODs, distances, recombination ratios...) is computed at load time. So we can directly try to group the markers in linkage groups. This is done using the group command that specifies a distance and a LOD threshold: two markers whose 2 point distance (Haldane/Ray) is below the given distance threshold and whose 2 points LOD is above the LOD threshold will be put in the same linkage group. Users that don't want to use one of the two thresholds can simply set the threshold they want to ignore to an extreme value (distance threshold set to zero, LOD threshold set to an arbitrary large number).
Let's try this with a 30cM distance threshold and a 
LOD
threshold:
CG> group 0.3 3.0
Linkage Groups :
---------------:
LOD threshold=3.00
Distance threshold=30.00:
Group ID : Marker ID List ...
1 : 275
2 : 197
3 : 139
4 : 128 281 259 178 146
5 : 86 265 243 192 116
6 : 54 307 304 295 289 201 177 150 102 96 67
7 : 47 236 48
8 : 30 249 248 234 223 210 173 80 172 287 167 120
9 : 21 303 282 279 242 202 200 185 61 170 26 228 226 224 196 183 16...
10 : 20 284 277 255 220 239 186 132 99 94 75 85 62 42 38
11 : 18 306 302 305 272 166 131 187 269 271 250 237 144 176 133 90 1...
12 : 17 266 260 257 254 231 247 114 207 225 212 199 188 122 55 110 1...
13 : 15 298 103 27 273 211 208 159 157 115 45 205 164 112
14 : 13 296 276 292 267 263 230 209 153 141 113 100 22 182 299 175 2...
15 : 10 204 245 191 190 184 179 240 221 154 127 123 155 92 91 89 57 ...
16 : 8 41
17 : 7 138 258 219 34 286 280 203 181 149 107 109 74 37 28 29 63
18 : 6 268 308 222 291 235 156 105 39 52 32 104 246 194 158 151 126 ...
19 : 5 262 216 147 117 97 88 12 218 293 300 274 232 171 270 229 206 ...
20 : 4 283 142 56 129 189 134 87 23 244 238 68
21 : 3 72 290 251 193 121 84 40 162 137 71 16 50 233 174
22 : 2 294 297 256 241 143 140 217 252 227 119 136 70 14 11 64
23 : 1 301 264 165 125 124 35 278 214 213 9 111 66 59 198
23
In this case, we get 23 groups. In the sequel we will work on the
group 10. To focus on this specific group, we will get the list of the
markers in the group using the groupget command and then
select them using the mrkselset command. This can be achieved
easyly in the graphical interface with a few clicks. If you use the
shell, do as follows:
CG> groupget 10 20 284 277 255 220 239 186 132 99 94 75 85 62 42 38To automagically select the markers of the group, one can use the following syntax (using
and ![$]$](img4.png){kind=small}
) that simply replaces what appears
between and with the result of the command in between (this is
called a macro-expansion). We can therefore select the group 10 with
the following command:
CG> mrkselset [groupget 10]Note that the current marker selection is not only a set of markers but also a default markers ordering. We can look at the LOD matrix beetween each pair of markers using the mrklod2p command.
CG> mrklod2p
20 284 277 255 220 239 186 132 99 94 75...
L029 A079 A059 A036 M232 D022 M237 M030 M076 M034 T018...
-----------------------------------------------------------------...
L029 |------ 4.4 5.5 1.1 4.4 6.3 2.0 4.0 2.0 1.1 3.6...
A079 | 4.4 ------ 18.4 7.4 16.5 5.7 10.5 21.7 10.5 7.4 14.0...
A059 | 5.5 18.4 ------ 6.2 14.2 6.4 9.0 17.8 9.0 6.2 11.9...
A036 | 1.1 7.4 6.2 ------ 9.0 2.6 13.0 7.7 13.0 21.4 8.6...
M232 | 4.4 16.5 14.2 9.0 ------ 4.8 13.0 16.0 13.0 9.0 17.8...
D022 | 6.3 5.7 6.4 2.6 4.8 ------ 3.2 5.2 3.2 2.6 4.5...
M237 | 2.0 10.5 9.0 13.0 13.0 3.2 ------ 11.0 19.9 13.0 12.8...
M030 | 4.0 21.7 17.8 7.7 16.0 5.2 11.0 ------ 11.0 7.7 13.5...
M076 | 2.0 10.5 9.0 13.0 13.0 3.2 19.9 11.0 ------ 13.0 12.8...
M034 | 1.1 7.4 6.2 21.4 9.0 2.6 13.0 7.7 13.0 ------ 8.6...
T018 | 3.6 14.0 11.9 8.6 17.8 4.5 12.8 13.5 12.8 8.6 -----...
T035 | 13.6 7.2 8.8 2.6 7.4 9.6 4.0 6.8 4.0 2.6 6.5...
L078 | 13.9 6.9 8.4 2.5 7.1 9.8 3.9 6.5 3.9 2.5 6.2...
L001 | 5.9 16.8 19.9 6.6 15.1 6.4 9.6 16.3 9.6 6.6 12.8...
L010 | 18.1 4.3 5.5 1.3 4.3 5.4 2.2 3.9 2.2 1.3 3.5...
Two-points LOD are also used in the mrkdouble command which
detects pairs of markers that have compatible genotypes on each
individuals. Such pairs of markers should be merged in one marker to
simplify the search for an optimal map. See the 1.8 section on
this topic. In practice, two markers can be compatible on all
individuals and nevertheless be unlinked. In this case they should not
be merged together.
CG> mrkdouble
Possible double markers:
L029 = L010 [18.1]
A079 = M030 [21.7]
A036 = M034 [21.4]
M237 = M076 [19.9]
T035 = L078 [21.4]
You see that 5 pairs of markers are ``double markers''. We will ignore
this issue for now and work on the whole group.
We can also have a look to the 2-points distance matrix using the mrkdist2p command. Haldane (h) or Kosambi (k) can be used. Ray distance is automatically selected for radiated hybrid data (whether you specify h or k).
CG> mrkdist2p h
Print two points distance matrices of the loci selection :
---------------------------------------------------------:
Data Set Number 1 :
L029 A079 A059 A036 M232 D022 M237 M030 M076 M03...
----------------------------------------------------------...
L029 |------ 29.9 25.3 61.8 28.2 10.0 43.4 31.1 43.4 61....
A079 | 29.9 ------ 2.2 17.9 3.4 13.2 10.0 0.0 10.0 17....
A059 | 25.3 2.2 ------ 21.6 5.9 10.6 13.0 2.3 13.0 21....
A036 | 61.8 17.9 21.6 ------ 13.0 29.8 5.9 16.6 5.9 0....
M232 | 28.2 3.4 5.9 13.0 ------ 15.9 5.9 3.5 5.9 13....
D022 | 10.0 13.2 10.6 29.8 15.9 ------ 22.5 13.9 22.5 29....
M237 | 43.4 10.0 13.0 5.9 5.9 22.5 ------ 8.8 0.0 5....
M030 | 31.1 0.0 2.3 16.6 3.5 13.9 8.8 ------ 8.8 16....
M076 | 43.4 10.0 13.0 5.9 5.9 22.5 0.0 8.8 ------ 5....
M034 | 61.8 17.9 21.6 0.0 13.0 29.8 5.9 16.6 5.9 ----...
T018 | 30.5 4.9 7.6 12.2 1.2 16.0 4.9 5.0 4.9 12....
T035 | 6.0 18.4 14.8 40.0 16.7 2.4 27.4 18.9 27.4 40....
L078 | 5.9 19.6 16.1 41.5 18.0 2.4 28.9 20.3 28.9 41....
L001 | 23.4 3.4 1.1 19.8 4.6 10.4 11.5 3.5 11.5 19....
L010 | 0.0 26.3 21.4 51.1 24.3 6.5 36.8 27.4 36.8 51....
You can also look to 2-points recombination ratio (breakage ratio for
RH data) using mrkfr2p:
CG> mrkfr2p
Print two points recombination fractions matrices of the loci selection :
---------------------------------------------------------------------------:
L029 A079 A059 A036 M232 D022 M237 M030 M076 M034 T018 T...
--------------------------------------------------------------------...
L029 |------ 0.2 0.2 0.4 0.2 0.1 0.3 0.2 0.3 0.4 0.2 ...
A079 | 0.2 ------ 0.0 0.2 0.0 0.1 0.1 0.0 0.1 0.2 0.0 ...
A059 | 0.2 0.0 ------ 0.2 0.1 0.1 0.1 0.0 0.1 0.2 0.1 ...
A036 | 0.4 0.2 0.2 ------ 0.1 0.2 0.1 0.1 0.1 0.0 0.1 ...
M232 | 0.2 0.0 0.1 0.1 ------ 0.1 0.1 0.0 0.1 0.1 0.0 ...
D022 | 0.1 0.1 0.1 0.2 0.1 ------ 0.2 0.1 0.2 0.2 0.1 ...
M237 | 0.3 0.1 0.1 0.1 0.1 0.2 ------ 0.1 0.0 0.1 0.0 ...
M030 | 0.2 0.0 0.0 0.1 0.0 0.1 0.1 ------ 0.1 0.1 0.0 ...
M076 | 0.3 0.1 0.1 0.1 0.1 0.2 0.0 0.1 ------ 0.1 0.0 ...
M034 | 0.4 0.2 0.2 0.0 0.1 0.2 0.1 0.1 0.1 ------ 0.1 ...
T018 | 0.2 0.0 0.1 0.1 0.0 0.1 0.0 0.0 0.0 0.1 ------ ...
T035 | 0.1 0.2 0.1 0.3 0.1 0.0 0.2 0.2 0.2 0.3 0.2 --...
L078 | 0.1 0.2 0.1 0.3 0.2 0.0 0.2 0.2 0.2 0.3 0.2 ...
L001 | 0.2 0.0 0.0 0.2 0.0 0.1 0.1 0.0 0.1 0.2 0.1 ...
L010 | 0.0 0.2 0.2 0.3 0.2 0.1 0.3 0.2 0.3 0.3 0.2 ...
Thomas Schiex
2009-10-27