Description Usage Arguments Value Author(s) References See Also Examples
Identification of interesting (high order) SNP interactions. The algorithm works on categorical data with binary response and delivers multi-valued logic expressions in disjunctive normal form typically explaining subsets of the data and an interaction tree containing interesting interactions.
1 2 | GPASInteractions(resp, preds, runs = 1, generations = 10000,
savegraph = "interactions.dot",occurences=10,ratio=0.1)
|
resp |
Vector with the response variables |
preds |
Matrix or data frame with the predictors |
runs |
Number of independent runs of GPAS |
generations |
Number of generations after which the algorithm will be stopped |
savegraph |
Name of the file the resulting GraphViz graph will be saved to |
occurences |
The minimum number of times an interaction has to occur to be included in the graph |
ratio |
The minimal ratio a single literal has to occur in relation to his ancestor in the interaction graph to be included in the interaction graph |
Returns an object of class GPAS
with a data.frame
in its slot summary
containing information about the last population of the executed runs.
For each individual in the last population the following information is contained:
run |
The run the individual was found in |
generation |
The generation the individual was created in |
objective value 1 |
Sum of correctly predicted cases and controls |
objective value 2 |
Correctly predicted controls |
objective value 3 |
Length of the individual |
individual |
A string representation of the individual |
Robin Nunkesser Robin.Nunkesser@hshl.de
R. Nunkesser, T. Bernholt, H. Schwender, K. Ickstadt, and I. Wegener (2007). Detecting High-Order Interactions of Single Nucleotide Polymorphisms Using Genetic Programming. Bioinformatics, 23, 3280-3288.
GraphViz: http://www.graphviz.org/
1 2 3 4 5 | # load example data
data(data.logicfs)
# execute GPAS to search for interesting interactions
GPASInteractions(cl.logicfs,data.logicfs,runs=1,generations=1000)
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