Tries to heuristically build a good framework map, i.e., a map such that all alternatives orders have a log-likelihood not within a given threshold of the framework map. The command may also be used to build comprehensive maps (including all markers) by adjusting thresholds.
The CarthaGene buildfw command is invoked as either one of :
Then, each available locus is tentatively inserted at each possible position. If there is no locus that provides a difference in log-likelihood larger than the AddThres threshold, the algorithm stops. If there are many orders for which the difference of log-likelihood is larger than the KeepThres Threshold, they are kept for the next step. The MrkTest flag indicates if post-processing is applied. If it is set to 0 no post-processing occurs. If it is set to 1, each remaining locus is tentatively inserted at each position in the previously built framework map and the difference in log-likelihood between each possible insertion and the best one (denoted by a '+') is reported. If it set to 2, no framework is built in the previous stage, instead the MrkList list of loci is used and the same post-processing as above applies. If the MrkTest equals 0 or 1, the framework's markers become the list of currently active markers.
When MrkTest flag is different from 0, further information on the remaining markers that have not been integrated in the map is provided in a table. Each remaining marker is represented on a line. The information is displayed in 6 group of columns.
BuildFW, remaining loci test : | | | | Lod2pt Dist2pt | 1 2 3 4 5 6 7 8 | Left<-M->Right Left<-M->Right | 0->N N->M | Weight Nb:W<AM Id | Name --|------------------|--------------------------------|--------------|---------------------|------- M1702 | + 0 | 2.16 23.97 115.1 2.5 | 680.8 106.7 | 0 2 9 | M1702
From left to right, we get:
When merged datasets are used, the two-points distances reported are computed only on informative data-sets and averaged among the informative data-sets. When RH data is used, and because different irradiation level (or mixed RH/genetic data) may have been used, distances are not averaged: only the first dataset merged is used.
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. # we first load a data set CG> dsload Data/rh.cg {1 haploid RH 53 118 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/rh.cg} # we perform linkage group detection (output omitted) CG> group 0.3 3 ... # we select the group 10 CG> mrkselset [groupget 10] # we build a framework map for this group CG> buildfw 3 3 {} 1 BuildFW, Adding Threshold = 3.00, Saving Threshold = 3.00. >>> Delta = 6.89 : Map 0 : log10-likelihood = -66.75 -------: Set : Marker List ... 1 : G7 G12 G16 >>> Delta = 6.30 , Id = 32, Locus = G18 : Map 0 : log10-likelihood = -80.72 -------: Set : Marker List ... 1 : G7 G12 G16 G18 >>> Delta = 7.04 , Id = 28, Locus = G14 : Map 0 : log10-likelihood = -93.15 -------: Set : Marker List ... 1 : G7 G12 G16 G18 G14 BuildFW, remaining loci test : | | | 2 2 3 3 2 | Lod2pt Dist2pt | 1 6 0 2 8 | Left<-M->Right Left<-M->Right | 0->N N->M | Weigh... --|------------|--------------------------------|--------------|------... G5 | 3 1 + | 13.70 - 29.6 - | 91.9 29.6 | 4... G17 | 2 + 0 | 18.05 15.66 21.1 25.3 | 72.0 9.0 | 2... G13 | + 3 | 20.41 22.03 14.6 10.6 | 30.4 12.7 | 3... G6 | + 0 | 16.23 20.68 25.7 14.6 | 30.4 14.0 | 0... # and check its reliability (any map at less than 3 LOD ?) CG> flips 4 3 0 Single Flip(window size : 4, threshold : 3.00). Map -1 : log10-likelihood = -93.15 -------: Set : Marker List ... 1 : G7 G12 G16 G18 G14 2 2 3 3 2 log10 1 6 0 2 8 -93.15 # no.
Thomas Schiex 2018-03-23