Sets the reliability testing threshold for framework maps.
The cgrobustness command is invoked as either:
The cgrobustness command sets the threshold used to verify if the current best known map is robust or not. A map is not robust if there exists another map such that , where is the multipoint log-likelihood of . A common value for the threshold is . When robustness checking is activated, each time a new map is inserted into the heap, the system verifies if the current best map is still robust. If not then it will stop any running search procedure because it has found a proof that the best known map is not robust enough. This is typically used when checking the reliability of a framework map using a cpu-intensive command such as flips or greedy in order to stop the search process as soon as the unreliability is proven.
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/bc.cg {1 f2 backcross 20 208 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/b... CG> buildfw 3 3 {} 1 BuildFW, Adding Threshold = 3.00, Saving Threshold = 3.00. >>> Delta = 46.28 : Map 0 : log10-likelihood = -14.70 -------: Set : Marker List ... 1 : MS8 MS10 MS14 BuildFW, remaining loci test : | | | 1 1 | Lod2pt Dist2pt | 8 0 4 | Left<-M->Right Left<-M->Right | 0->N N->M | Weight Nb... --|--------|--------------------------------|--------------|----------... MS1 |2 2 + | -0.00 - 345.4 - | 15.5 345.4 | 4 ... MS2 |+ 3 2 | - 15.26 - 23.8 | - 23.8 | 5 ... MS3 |+ 3 | - 15.07 - 25.5 | - 25.5 | 3 ... MS4 |+ 1 2 3 | - 22.84 - 14.5 | - 14.5 | 6 ... MS5 | + 1 2 | 12.33 4.02 14.2 5.6 | 0.0 2.3 | 3 ... MS6 | 3 1 + | 1.05 - 22.6 - | 15.5 22.6 | 4 ... MS7 |2 + 1 3 | 35.05 5.05 5.7 10.8 | 0.0 1.1 | 6 ... MS9 | + 0 1 | 40.82 7.22 1.9 0.0 | 0.0 3.3 | 1 ... MS11 | 1 0 + | 3.61 - 0.0 - | 15.5 0.0 | 1 ... MS12 | 2 0 + | 3.61 - 0.0 - | 15.5 0.0 | 2 ... MS13 | 0 + | 6.02 - 0.0 - | 15.5 0.0 | 0 ... MS15 | 3 0 + | 0.00 - 345.4 - | 15.5 345.4 | 3 ... MS16 | 2 0 + | 3.61 - 0.0 - | 15.5 0.0 | 2 ... MS17 | + 0 | 1.09 1.51 31.8 0.0 | 3.3 12.2 | 0 ... MS18 | 2 + | 0.00 - 345.4 - | 15.5 345.4 | 2 ... MS19 |1 3 + | 0.45 - 34.7 - | 15.5 34.7 | 4 ... MS20 | 3 + | 0.71 - 45.8 - | 15.5 45.8 | 3 ... CG> cgrobustness -5 CG> greedy 1 0 1 20 0 Map -1 : log10-likelihood = -14.70 -------: Set : Marker List ... 1 : MS8 MS10 MS14 Run number 0 Current best map is not robust! Aborted! CG> heapsize 3 CG> heaprint Map 0 : log10-likelihood = -60.98 -------: Set : Marker List ... 1 : MS10 MS8 MS14 Map 1 : log10-likelihood = -17.48 -------: Set : Marker List ... 1 : MS8 MS14 MS10 Map 2 : log10-likelihood = -14.70 -------: Set : Marker List ... 1 : MS8 MS10 MS14 CG>
Thomas Schiex 2018-03-23