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 :

   CarthaGene version 1.2-LKH, Copyright (c) 1997-2010 (INRA).

   CarthaGene comes with ABSOLUTELY NO WARRANTY.
   CarthaGene is free software. You are welcome to redistribute it,
   under certain conditions. See the License file for information.

Type 'help' for help.

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

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 (29): 160 159 158 151 143 141 137 136 135 174 168 167 179 182 183 185 188...
8 (25): 160 168 169 172 178 183 185 193 204 206 209 208 213 216 215 224 239...
9 (38): 1 424 411 407 398 386 379 368 358 340 336 2 314 304 300 299 292 291...
10 (34): 83 84 87 92 102 106 109 114 115 135 168 178 183 196 199 206 212 22...
11 (35): 1 423 411 386 379 366 365 337 329 315 291 287 265 249 244 225 215 ...
12 (16): 77 84 86 98 99 106 110 124 170 182 185 192 199 208 349 363
13 (2): 44 367
14 (16): 49 57 64 138 151 167 191 205 208 249 287 291 331 340 360 363
15 (2): 44 67

Map -1 : log10-likelihood =  -312.88
-------:
 Set : Marker List ...
   1 : 1 424 411 407 398 386 379 368 358 340 336 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 (2.5.22)