Man pages for galgo
Genetic Algorithms for Multivariate Statistical Models from Large-Scale Functional Genomics Data
| activeChromosomeSet.BigBang | Focus the analysis to different sets of chromosomes |
| addCount.BigBang | Add a chromosome to rank and frequency stability counting |
| addRandomSolutions.BigBang | Adds random pre-existed solutions |
| addSolutions.BigBang | Adds user-built or external chromosomes as solutions |
| ALL | Acute Lymphoblastic Leukemia data (Yeoh et. al., 2002) for... |
| ALL.classes | Acute Lymphoblastic Leukemia data (Yeoh et. al., 2002) for... |
| as.double.Chromosome | Converts the chromosome values (genes) to its numerical... |
| as.double.Gene | Converts the gene parameters (shape1, shape2) to its... |
| as.double.Niche | Converts the chromosome values (genes) to a vector |
| as.list.Object | Convert a variable of class Object to a list |
| as.matrix.BigBang | Prints the representation of the BigBang object |
| as.matrix.Gene | Converts the gene parameters (shape1, shape2) to matrix |
| as.matrix.Niche | Converts the chromosome values (genes) to a matrix |
| assignParallelFile.BigBang | Assigns a different saveFile value for parallelization |
| Bag | A list-like Object |
| bestFitness.Galgo | Returns the fitness of the best chromosome |
| bestFitness.Niche | Returns the fitness of the best chromosome in the niche |
| bestFitness.World | Returns the fitness of the best chromosome |
| best.Galgo | Returns the best chromosome |
| best.Niche | Returns the best chromosome of the niche |
| best.World | Returns the best chromosome |
| BigBang | Represents the ensemble of the results of evolving several... |
| blast.BigBang | Evolves Galgo objects saving the results for further analysis |
| buildCount.BigBang | Builds the rank and frequency stability counting |
| Chromosome | The representation of a set of genes for genetic algorithms |
| classPrediction | Function used to predict class evaluating a fitness function... |
| classPredictionMatrix.BigBang | Predicts class for samples from chromosomes |
| clone.Chromosome | Clones itself and its genes |
| clone.Galgo | Clones itself and all its objects |
| clone.Niche | Clones itself and its chromosomes |
| clone.World | Clones itself and its niches |
| computeCount.BigBang | Compute the counts for every gene from a set of chromosomes. |
| configBB.VarSel | Creates and configure all objects needed for a "variable... |
| configBB.VarSelMisc | Creates and configure all objects needed for a "variable... |
| confusionMatrix.BigBang | Computes the class confusion matrix from a class prediction... |
| crossover.Niche | Performs crossover between chromosomes of the niche |
| decode.Chromosome | Converts the gene values to user-readable values |
| distanceImportanceNetwork.BigBang | Converts geneImportanceNetwork matrix to distance matrix |
| evaluate.Galgo | Evaluates all chromosomes with a fitness function |
| evaluate.Niche | Evaluates the chromosome using a fitness function |
| evaluate.World | Evaluate all niches with a fitness function |
| evolve.Galgo | Evolves the chromosomes populations of a Galgo (Genetic... |
| filterSolution.BigBang | Filters solutions |
| fitness | Function used to evaluate a chromosome |
| fitnessSplits.BigBang | Computes the fitness function from chromosomes for different... |
| formatChromosome.BigBang | Converts chromosome for storage in BigBang object |
| forwardSelectionModels.BigBang | Gets the "best" models using top-ranked genes and a... |
| Galgo | The representation of a Genetic Algorithm |
| galgo.dist | Computes the distance in GALGO for KNN based methods |
| galgo-package | Galgo perform feature selection from large scale data. |
| Gene | The representation of a gene in a chromosome for genetic... |
| geneBackwardElimination | Searches for shorter or better models using backward... |
| geneCoverage.BigBang | Computes the fraction of genes present in the top-rank from... |
| geneFrequency.BigBang | Computes the frequency of genes based on chromosomes |
| geneImportanceNetwork.BigBang | Computes the number of times a couple of top-ranked-genes are... |
| geneRankStability.BigBang | Computes the rank history for top-ranked genes |
| generateRandom.Chromosome | Generates random values for all genes in the chromosome |
| generateRandom.Galgo | Generates random values for all populations in the Galgo... |
| generateRandom.Gene | Generates a random value from the defined function |
| generateRandomModels | Generates Random shorter models |
| generateRandom.Niche | Generates random values for all genes contained in all... |
| generateRandom.World | Generates random values for all niches in the world |
| genes.Chromosome | Converts the genes values to a numeric vector |
| getFitness.Niche | Returns the fitness vector related to chromosomes |
| getFrequencies.BigBang | Computes gene freqencies |
| heatmapModels.BigBang | Plots models using heatmap plot |
| knn_C_predict | Class prediction using KNN method calling the C code |
| knn_R_predict | Class prediction using KNN method calling the R code |
| length.Bag | Gets the length of the object as its list version |
| length.Chromosome | Gets the number of genes defined in the chromosome |
| length.Galgo | Gets the number of populations defined in the Galgo object |
| length.Niche | Gets the number of chromosomes defined in the niche |
| length.World | Gets the number of niches defined in the world |
| loadObject | Load saved data of class Object and use reObject as necessary |
| loadParallelFiles.BigBang | Load all files saved during the parallelization |
| maxFitness.Galgo | Returns the fitness of the maximum chromosome |
| maxFitness.Niche | Returns the fitness of the maximum chromosome in the niche |
| maxFitness.World | Returns the fitness of the maximum chromosome |
| max.Galgo | Returns the chromosome whose current fitness is maximum |
| max.Niche | Returns the chromosome in the niche whose current fitness is... |
| max.World | Returns the chromosome whose current fitness is maximum |
| meanFitness.BigBang | Computes the "mean" fitness from several solutions |
| meanGeneration.BigBang | Computes the mean number of generations requiered to reach a... |
| mergeBangs.BigBang | Merges the information from other BigBang objects |
| mlhd_C_predict | Class prediction using Maximum Likelihood Discriminant... |
| mlhd_R_predict | Class prediction using Maximum Likelihood Discriminant... |
| modelSelection | Function used to evaluate a fitness function in many... |
| mutate.Chromosome | Mutates a chromosome in specific positions |
| mutate.Gene | Mutates a gene |
| mutate.Niche | Mutates a niche calling mutate method for all chromosomes |
| nearcent_C_predict | Class prediction using the nearest centroid method calling... |
| nearcent_R_predict | Class prediction using the nearest centroid method calling... |
| newCollection.Chromosome | Generates a list of chromosomes cloning the original... |
| newCollection.Gene | Generates a list of cloned objects |
| newCollection.Niche | Generates a list of cloned niches |
| newCollection.World | Generates a list cloning an object |
| newRandomCollection.Chromosome | Creates a list of cloned chromosomes object with its internal... |
| newRandomCollection.Gene | Generates a list of cloned objects and random values |
| newRandomCollection.Niche | Creates a list of cloned niches with its internal values... |
| newRandomCollection.World | Creates a list of cloned object with its internal values... |
| Niche | The representation of a set of chromosomes for genetic... |
| nnet_R_predict | Class prediction using the neural networks method calling the... |
| offspring.Niche | Overwrites the new niche selecting a new population from the... |
| pcaModels.BigBang | Plots models in principal components space |
| plot.BigBang | Plots about the collected information in a BigBang object |
| plot.Galgo | Plots information about the Galgo object |
| plot.Niche | Plots information about niche object |
| plot.World | Plots information about world object |
| predict.BigBang | Predicts the class or fitting of new set of samples |
| print.Bag | Prints the representation of the Bag object |
| print.BigBang | Prints the representation of a BigBang object |
| print.Chromosome | Prints the representation of the chromosome object |
| print.Galgo | Prints the representation of a Galgo object |
| print.Gene | Prints the representation of a gene object |
| print.Niche | Prints the representation of a niche object |
| print.World | Prints the representation of a world object |
| progeny.Niche | Performs offspring, crossover, mutation, and elitism... |
| progeny.World | Calls progeny method to all niches in the world object |
| randomforest_R_predict | Class prediction using RandomForest method calling the R code |
| refreshStats.Galgo | Updates the internal values from the current populations |
| refreshStats.Niche | Updates the internal values from the current population |
| refreshStats.World | Updates the internal statistics from the current population |
| reInit.Chromosome | Erases all internal values in order to re-use the object |
| reInit.Galgo | Erases all internal values in order to re-use the object |
| reInit.Gene | Erases all internal values in order to re-use the object |
| reInit.Niche | Erases all internal values in order to re-use the object |
| reInit.World | Erases all internal values in order to re-use the world... |
| reObject | Creates proper extended Object from a list obtained by... |
| robustGeneBackwardElimination | Searches for shorter or better models using backward... |
| rpart_R_predict | Class prediction using the recursive tree partitions method... |
| runifInt | Generation of random uniform integer values |
| saveObject.BigBang | Saves the BigBang object into a file in a suitable format |
| scaling.Niche | Assigns a weight for every chromosome to be selected for the... |
| sensitivityClass.BigBang | Computes the sensitivity of class prediction |
| specificityClass.BigBang | Computes the specificity of class prediction |
| summary.Bag | Prints the representation of the Bag object |
| summary.BigBang | Prints the representation of the BigBang object |
| summary.Chromosome | Prints the representation of the chromosome object and all... |
| summary.Galgo | Prints the representation and statistics of the galgo object |
| summary.Gene | Prints the representation of a gene object |
| summary.Niche | Prints the representation and statistics of the niche object |
| summary.World | Prints the representation and statistics of the world object |
| svm_C_predict | Class prediction using support vector machines method calling... |
| svm_R_predict | Class prediction using support vector machines method calling... |
| unObject.Object | Converts variables from class Object (and derived classes) to... |
| World | The representation of a set of niches with migration for... |
