Man pages for galgo
Genetic Algorithms for Multivariate Statistical Models from Large-Scale Functional Genomics Data

activeChromosomeSet.BigBangFocus the analysis to different sets of chromosomes
addCount.BigBangAdd a chromosome to rank and frequency stability counting
addRandomSolutions.BigBangAdds random pre-existed solutions
addSolutions.BigBangAdds user-built or external chromosomes as solutions
ALLAcute Lymphoblastic Leukemia data (Yeoh et. al., 2002) for...
ALL.classesAcute Lymphoblastic Leukemia data (Yeoh et. al., 2002) for...
as.double.ChromosomeConverts the chromosome values (genes) to its numerical...
as.double.GeneConverts the gene parameters (shape1, shape2) to its...
as.double.NicheConverts the chromosome values (genes) to a vector
as.list.ObjectConvert a variable of class Object to a list
as.matrix.BigBangPrints the representation of the BigBang object
as.matrix.GeneConverts the gene parameters (shape1, shape2) to matrix
as.matrix.NicheConverts the chromosome values (genes) to a matrix
assignParallelFile.BigBangAssigns a different saveFile value for parallelization
BagA list-like Object
bestFitness.GalgoReturns the fitness of the best chromosome
bestFitness.NicheReturns the fitness of the best chromosome in the niche
bestFitness.WorldReturns the fitness of the best chromosome
best.GalgoReturns the best chromosome
best.NicheReturns the best chromosome of the niche
best.WorldReturns the best chromosome
BigBangRepresents the ensemble of the results of evolving several...
blast.BigBangEvolves Galgo objects saving the results for further analysis
buildCount.BigBangBuilds the rank and frequency stability counting
ChromosomeThe representation of a set of genes for genetic algorithms
classPredictionFunction used to predict class evaluating a fitness function...
classPredictionMatrix.BigBangPredicts class for samples from chromosomes
clone.ChromosomeClones itself and its genes
clone.GalgoClones itself and all its objects
clone.NicheClones itself and its chromosomes
clone.WorldClones itself and its niches
computeCount.BigBangCompute the counts for every gene from a set of chromosomes.
configBB.VarSelCreates and configure all objects needed for a "variable...
configBB.VarSelMiscCreates and configure all objects needed for a "variable...
confusionMatrix.BigBangComputes the class confusion matrix from a class prediction...
crossover.NichePerforms crossover between chromosomes of the niche
decode.ChromosomeConverts the gene values to user-readable values
distanceImportanceNetwork.BigBangConverts geneImportanceNetwork matrix to distance matrix
evaluate.GalgoEvaluates all chromosomes with a fitness function
evaluate.NicheEvaluates the chromosome using a fitness function
evaluate.WorldEvaluate all niches with a fitness function
evolve.GalgoEvolves the chromosomes populations of a Galgo (Genetic...
filterSolution.BigBangFilters solutions
fitnessFunction used to evaluate a chromosome
fitnessSplits.BigBangComputes the fitness function from chromosomes for different...
formatChromosome.BigBangConverts chromosome for storage in BigBang object
forwardSelectionModels.BigBangGets the "best" models using top-ranked genes and a...
GalgoThe representation of a Genetic Algorithm
galgo.distComputes the distance in GALGO for KNN based methods
galgo-packageGalgo perform feature selection from large scale data.
GeneThe representation of a gene in a chromosome for genetic...
geneBackwardEliminationSearches for shorter or better models using backward...
geneCoverage.BigBangComputes the fraction of genes present in the top-rank from...
geneFrequency.BigBangComputes the frequency of genes based on chromosomes
geneImportanceNetwork.BigBangComputes the number of times a couple of top-ranked-genes are...
geneRankStability.BigBangComputes the rank history for top-ranked genes
generateRandom.ChromosomeGenerates random values for all genes in the chromosome
generateRandom.GalgoGenerates random values for all populations in the Galgo...
generateRandom.GeneGenerates a random value from the defined function
generateRandomModelsGenerates Random shorter models
generateRandom.NicheGenerates random values for all genes contained in all...
generateRandom.WorldGenerates random values for all niches in the world
genes.ChromosomeConverts the genes values to a numeric vector
getFitness.NicheReturns the fitness vector related to chromosomes
getFrequencies.BigBangComputes gene freqencies
heatmapModels.BigBangPlots models using heatmap plot
knn_C_predictClass prediction using KNN method calling the C code
knn_R_predictClass prediction using KNN method calling the R code
length.BagGets the length of the object as its list version
length.ChromosomeGets the number of genes defined in the chromosome
length.GalgoGets the number of populations defined in the Galgo object
length.NicheGets the number of chromosomes defined in the niche
length.WorldGets the number of niches defined in the world
loadObjectLoad saved data of class Object and use reObject as necessary
loadParallelFiles.BigBangLoad all files saved during the parallelization
maxFitness.GalgoReturns the fitness of the maximum chromosome
maxFitness.NicheReturns the fitness of the maximum chromosome in the niche
maxFitness.WorldReturns the fitness of the maximum chromosome
max.GalgoReturns the chromosome whose current fitness is maximum
max.NicheReturns the chromosome in the niche whose current fitness is...
max.WorldReturns the chromosome whose current fitness is maximum
meanFitness.BigBangComputes the "mean" fitness from several solutions
meanGeneration.BigBangComputes the mean number of generations requiered to reach a...
mergeBangs.BigBangMerges the information from other BigBang objects
mlhd_C_predictClass prediction using Maximum Likelihood Discriminant...
mlhd_R_predictClass prediction using Maximum Likelihood Discriminant...
modelSelectionFunction used to evaluate a fitness function in many...
mutate.ChromosomeMutates a chromosome in specific positions
mutate.GeneMutates a gene
mutate.NicheMutates a niche calling mutate method for all chromosomes
nearcent_C_predictClass prediction using the nearest centroid method calling...
nearcent_R_predictClass prediction using the nearest centroid method calling...
newCollection.ChromosomeGenerates a list of chromosomes cloning the original...
newCollection.GeneGenerates a list of cloned objects
newCollection.NicheGenerates a list of cloned niches
newCollection.WorldGenerates a list cloning an object
newRandomCollection.ChromosomeCreates a list of cloned chromosomes object with its internal...
newRandomCollection.GeneGenerates a list of cloned objects and random values
newRandomCollection.NicheCreates a list of cloned niches with its internal values...
newRandomCollection.WorldCreates a list of cloned object with its internal values...
NicheThe representation of a set of chromosomes for genetic...
nnet_R_predictClass prediction using the neural networks method calling the...
offspring.NicheOverwrites the new niche selecting a new population from the...
pcaModels.BigBangPlots models in principal components space
plot.BigBangPlots about the collected information in a BigBang object
plot.GalgoPlots information about the Galgo object
plot.NichePlots information about niche object
plot.WorldPlots information about world object
predict.BigBangPredicts the class or fitting of new set of samples
print.BagPrints the representation of the Bag object
print.BigBangPrints the representation of a BigBang object
print.ChromosomePrints the representation of the chromosome object
print.GalgoPrints the representation of a Galgo object
print.GenePrints the representation of a gene object
print.NichePrints the representation of a niche object
print.WorldPrints the representation of a world object
progeny.NichePerforms offspring, crossover, mutation, and elitism...
progeny.WorldCalls progeny method to all niches in the world object
randomforest_R_predictClass prediction using RandomForest method calling the R code
refreshStats.GalgoUpdates the internal values from the current populations
refreshStats.NicheUpdates the internal values from the current population
refreshStats.WorldUpdates the internal statistics from the current population
reInit.ChromosomeErases all internal values in order to re-use the object
reInit.GalgoErases all internal values in order to re-use the object
reInit.GeneErases all internal values in order to re-use the object
reInit.NicheErases all internal values in order to re-use the object
reInit.WorldErases all internal values in order to re-use the world...
reObjectCreates proper extended Object from a list obtained by...
robustGeneBackwardEliminationSearches for shorter or better models using backward...
rpart_R_predictClass prediction using the recursive tree partitions method...
runifIntGeneration of random uniform integer values
saveObject.BigBangSaves the BigBang object into a file in a suitable format
scaling.NicheAssigns a weight for every chromosome to be selected for the...
sensitivityClass.BigBangComputes the sensitivity of class prediction
specificityClass.BigBangComputes the specificity of class prediction
summary.BagPrints the representation of the Bag object
summary.BigBangPrints the representation of the BigBang object
summary.ChromosomePrints the representation of the chromosome object and all...
summary.GalgoPrints the representation and statistics of the galgo object
summary.GenePrints the representation of a gene object
summary.NichePrints the representation and statistics of the niche object
summary.WorldPrints the representation and statistics of the world object
svm_C_predictClass prediction using support vector machines method calling...
svm_R_predictClass prediction using support vector machines method calling...
unObject.ObjectConverts variables from class Object (and derived classes) to...
WorldThe representation of a set of niches with migration for...
galgo documentation built on Oct. 14, 2018, 5:04 p.m.