GPASInteractions: Execute the GPAS algorithm for feature selection

In RFreak: R/FrEAK interface

Description

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.

Usage

GPASInteractions(resp, preds, runs = 1, generations = 10000, 
  savegraph = "interactions.dot",occurences=10,ratio=0.1)

Arguments

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

Value

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

Author(s)

Robin Nunkesser [e-mail]

References

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/

See Also

"GPAS", GPASDiscrimination

Examples

# load example data
data(data.logicfs)

# execute GPAS to search for interesting interactions
GPASInteractions(cl.logicfs,data.logicfs,runs=1,generations=1000)

RFreak documentation built on May 1, 2019, 10:53 p.m.