Subsections
paretoplotg
Draw the Pareto frontier.
The paretoplotg command is invoked as:
The paretoplotg command gives a graphical view of the Pareto frontier (that can be zoomed (Ctrl+Up), printed or saved (right mouse click)). It draws the traditional and comparative mapping criteria for the maps in the frontier. The red triangle corresponds to the best map. By clicking on any point in the frontier, a comparative mapping view can be obtained between the corresponding map and the reference genome. The distance between adjacent markers can be fixed or proportional, see the option menu with a right mouse click.
This important command allows to assess the quality of the Pareto frontier and the comparative mapping strategy. First, the frontier should be dense, i.e. having at most one map per number of breakpoints, and without too many dominated maps (represented by the green points) (if not, then try to increase the NbResolution parameter in paretolkh and the Anytime parameter in paretogreedy). Secondly, the shapes of the two loglikelihood curves show the respective contributions of the biological data and of the reference order in the selection of the best map. If the two curves are almost identical, then the contribution of the reference order is weak. On the contrary, if the curve of the comparative mapping criterion decreases rapidly, then the contribution of the reference order is strong. A flat curve means that the selection of the best map which maximizes the comparative mapping criterion is not very reliable.
- Lambda : it corresponds to the expected number of breakpoints between the true order and the reference order. If unknown, it should be set to 1 or to the minimum number of obligate breakpoints (the number of segments minus one in the order dataset) if greater than one.
Nothing.
Thomas Schiex
2009-10-27
