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The CARPET package [8] Com&Easy function was used with the following settings:parameter set: Principal table, variable p-value cut off for the ChIP-seq peaks; Secondary table, ChIP-chip peaks; Analysis type, common; Coordinate common, Principal Table.
Table 3 Algorithm settings Parameter Configuration Th1 0.97 Th2 0.98 Th3 2 Th4 3. Figures 5 and 6 show the results obtained in the simulations.
The only obligatory attribute of the settings parameter is the target attribute that defines the id of the HTML element the cluster heatmap is inserted in.
Then, the InCHlib object is instantiated with the settings parameter (given as the JavaScript object), the JSON file is read using the read_data_from_file method and the cluster heatmap is rendered by calling the draw method.
Table 1 Genetic algorithm's settings Parameter Value Population size 100 Maximum generations 100 Crossover probability 0.8 Mutation probability 0.01 Selection method Stochastic universal approximation (SUS) Crossover points 2 points.
Table 1 Relevant parameter settings Parameter Value Description w 0.5 Pixel width (m) λ 0.035 Width of weighting ellipse (m) α 4 Regularization parameter l 0.75 Threshold for calculate possible region (m).
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Independently of the previous settings, parameters are determined for Doxorubicin 60 mg/m and Docetaxel 75 mg/m using data sets 1, 4 8.
However, the model can be adapted to others settings provided parameter values are regionally specific.
Sample preparation, instrument settings and parameter characterization are described in detail in Costa et al. [ 7].
Simulation settings and parameters are summarized in Table 1.
The settings of parameters are shown in Table 2 [23].
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