framework

Builds a framework map (only on Linux computers).

Synopsis :

The CarthaGene framework command is invoked as either one of :

• framework Options
• framework ThresholdMin ThresholdMax Delta ChangeSel

Description :

The framework command builds a framework map by selecting a subset of the current markers based on constrained all-pairs shortest path algorithm. Two adjacent markers in the framework map have their contribution to the 2-pt log10-likelihood of the map lower than a threshold the value of which varies in the range $[ThresholdMin,ThresholdMax]$. The robustness of the resulting map is controlled by the parameter Delta. It ensures that it does not exist any other map containing the same set of markers and with a different order such that its 2-pt log10-likelihood is greater than the framework map likelihood minus Delta. For instance if Delta is equal to 3, then any other map is 1000 less likely. If ChangeSel is equal to 1 then the best framework map is inserted into the Carthagene heap.

Arguments :

• Options : -u to obtain the synopsis of the normal use, -h to print a one line description, -H to print a short help.
• ThresholdMin: the minimum threshold in log-likelihood for considering 2 adjacent markers.
• ThresholdMax: the maximum threshold in log-likelihood for considering 2 adjacent markers.
• Delta: the minimum difference in log-likelihood between the framework map and any other map with the same marker selection.
• ChangeSel: if equal to 1 then the best framework map is inserted into the Carthagene heap (modifying the current marker list).

Returns :

nothing.

Example :

CG> dsload Data/rh02_true.id
{1 haploid RH 427 88 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/rh0...
CG>

# merge markers with similar RH vectors
CG> mrkmerges
Markers 368 and 374 merged in 368.
Markers 369 and 368 merged in 369.
Markers 348 and 354 merged in 348.
Markers 349 and 351 merged in 349.
Markers 346 and 347 merged in 346.
Markers 367 and 370 merged in 367.
Markers 358 and 359 merged in 358.
Markers 350 and 352 merged in 350.
Markers 372 and 373 merged in 372.
Markers 375 and 380 merged in 375.
Markers 288 and 290 merged in 288.
Markers 295 and 296 merged in 295.
Markers 284 and 289 merged in 284.
Markers 249 and 250 merged in 249.
Markers 255 and 257 merged in 255.
Markers 258 and 260 merged in 258.
Markers 195 and 197 merged in 195.
Markers 214 and 217 merged in 214.
Markers 238 and 241 merged in 238.
Markers 229 and 230 merged in 229.
Markers 227 and 228 merged in 227.
Markers 186 and 187 merged in 186.
Markers 127 and 132 merged in 127.
Markers 127 and 133 merged in 127.
Markers 127 and 129 merged in 127.
Markers 125 and 127 merged in 125.
Markers 91 and 95 merged in 91.
Markers 94 and 91 merged in 94.
The two markers are incompatibles.
Markers 126 and 128 merged in 126.
Markers 126 and 131 merged in 126.
Markers 126 and 134 merged in 126.
Markers 150 and 153 merged in 150.
Markers 152 and 150 merged in 152.
Markers 144 and 145 merged in 144.
The two markers are incompatibles.
Markers 141 and 142 merged in 141.
Markers 79 and 80 merged in 79.
Markers 14 and 16 merged in 14.
Markers 110 and 111 merged in 110.
Markers 110 and 112 merged in 110.
Markers 117 and 118 merged in 117.
Markers 117 and 121 merged in 117.
Markers 116 and 117 merged in 116.
Markers 3 and 390 merged in 3.
Markers 3 and 391 merged in 3.
Markers 3 and 392 merged in 3.
Markers 3 and 399 merged in 3.
Markers 3 and 400 merged in 3.
Markers 3 and 401 merged in 3.
Markers 3 and 402 merged in 3.
Markers 3 and 403 merged in 3.
Markers 3 and 404 merged in 3.
Markers 3 and 405 merged in 3.
Markers 3 and 395 merged in 3.
Markers 3 and 393 merged in 3.
Markers 3 and 397 merged in 3.
Markers 3 and 396 merged in 3.
Markers 146 and 149 merged in 146.
Markers 155 and 156 merged in 155.
Markers 155 and 157 merged in 155.
Markers 169 and 171 merged in 169.
Markers 176 and 177 merged in 176.
Markers 164 and 165 merged in 164.
Markers 411 and 412 merged in 411.
Markers 416 and 417 merged in 416.
Markers 426 and 427 merged in 426.
Markers 421 and 425 merged in 421.
Markers 410 and 414 merged in 410.
Markers 376 and 382 merged in 376.
Markers 376 and 378 merged in 376.
The two markers are incompatibles.
Markers 375 and 381 merged in 375.
The two markers are incompatibles.
Markers 384 and 385 merged in 384.
The two markers are incompatibles.
Markers 188 and 189 merged in 188.
Markers 178 and 181 merged in 178.
Markers 180 and 178 merged in 180.
Markers 315 and 316 merged in 315.
Markers 315 and 322 merged in 315.
Markers 315 and 321 merged in 315.
Markers 315 and 317 merged in 315.
Markers 315 and 319 merged in 315.
Markers 343 and 344 merged in 343.
Markers 318 and 323 merged in 318.
The two markers are incompatibles.
The two markers are incompatibles.
Markers 340 and 342 merged in 340.
Markers 345 and 346 merged in 345.
Markers 324 and 325 merged in 324.
Markers 331 and 332 merged in 331.
The two markers are incompatibles.
Markers 326 and 327 merged in 326.
Markers 194 and 195 merged in 194.
Markers 279 and 280 merged in 279.
Markers 265 and 269 merged in 265.
Markers 265 and 266 merged in 265.
Markers 263 and 264 merged in 263.
Markers 265 and 271 merged in 265.
Markers 275 and 276 merged in 275.
Markers 245 and 249 merged in 245.
Markers 283 and 284 merged in 283.
Markers 267 and 268 merged in 267.

CG>

# build a framework map such that any other map is 100 less likely
# and update the current marker selection to this framework map
CG> frameworkn 3 15 2 1
All TSP costs multiplied by 1000.
3 (2): 124 130
4 (14): 298 302 301 303 304 305 307 311 310 315 324 328 329 326
5 (14): 298 302 301 303 304 305 307 311 310 315 324 328 329 326
6 (26): 297 295 300 301 307 310 315 324 2 334 335 339 343 348 355 360 366 3...
7 (32): 160 159 158 151 143 141 137 136 135 174 168 167 179 182 183 185 188...
8 (24): 160 168 169 172 180 183 190 200 199 201 208 209 212 219 229 239 244...
9 (36): 1 424 411 407 398 386 379 369 358 340 336 2 314 304 300 299 292 291...
10 (2): 83 423
11 (28): 1 386 379 366 365 337 329 315 291 287 265 258 242 210 201 199 194 ...
12 (22): 77 164 169 182 185 192 199 220 251 259 262 288 297 301 324 334 337...
13 (27): 44 23 20 4 46 51 57 64 67 69 71 75 73 82 83 87 99 103 216 244 259 ...
14 (2): 49 363
15 (2): 44 67

Map -1 : log10-likelihood =  -297.89
-------:
 Set : Marker List ...
   1 : 1 424 411 407 398 386 379 369 358 340 336 2 314 304 300 299 292 291 ...

CG>

See also:

• frameworkn (uses normalized 2-pt log10-likelihood)
• frameworkl (uses 2-pt LOD instead of 2-pt log10-likelihood)
• frameworkmst (2.5.21)