Uniform interfaces to R machine learning procedures for data in Bioconductor containers

Documentation for package ‘MLInterfaces’ version 1.87.0

Help Pages

-- A --

acc	Assessing classifier performance
acc-method	Assessing classifier performance
adaI	revised MLearn interface for machine learning

-- B --

baggingI	revised MLearn interface for machine learning
balKfold.xvspec	generate a partition function for cross-validation, where the partitions are approximately balanced with respect to the distribution of a response variable
BgbmI	revised MLearn interface for machine learning
blackboostI	revised MLearn interface for machine learning
brennan_2013_tabS7exc	Clinical characterization of 158 GBM samples from https://doi.org/10.1016/j.cell.2013.09.034 supp table S7

-- C --

classifierOutput-class	Class "classifierOutput"
classifOutput	MLInterfaces infrastructure
clusteringOutput-class	container for clustering outputs in uniform structure
clusteringSchema-class	container for clustering outputs in uniform structure
clustOutput	MLInterfaces infrastructure
confuMat	Compute the confusion matrix for a classifier.
confuMat-method	Compute the confusion matrix for a classifier.
confuMat-methods	Compute the confusion matrix for a classifier.
confuTab	Compute confusion tables for a confusion matrix.
cverrs	MLInterfaces infrastructure

-- D --

DAB	real adaboost (Friedman et al)
daboostCont-class	Class "raboostCont" ~~~
dlda	revised MLearn interface for machine learning
dlda2	revised MLearn interface for machine learning
dldaI	revised MLearn interface for machine learning

-- E --

es2df

MLInterfaces infrastructure

-- F --

F1	Assessing classifier performance
F1-method	Assessing classifier performance
fn	Assessing classifier performance
fn-method	Assessing classifier performance
fp	Assessing classifier performance
fp-method	Assessing classifier performance
fs.absT	support for feature selection in cross-validation
fs.probT	support for feature selection in cross-validation
fs.topVariance	support for feature selection in cross-validation
fsHistory	extract history of feature selection for a cross-validated machine learner
fsHistory-method	Class "classifierOutput"

-- G --

gbm2	revised MLearn interface for machine learning
getConverter	container for clustering outputs in uniform structure
getConverter-method	container for clustering outputs in uniform structure
getDist	container for clustering outputs in uniform structure
getDist-method	container for clustering outputs in uniform structure
getGrid	MLInterfaces infrastructure
getGrid-method	MLInterfaces infrastructure
getVarImp	Class "varImpStruct" - collect data on variable importance from various machine learning methods
getVarImp-method	Class "varImpStruct" - collect data on variable importance from various machine learning methods
glmI.logistic	revised MLearn interface for machine learning
groupIndex	MLInterfaces infrastructure

-- H --

hclustConverter	MLInterfaces infrastructure
hclustI	revised MLearn interface for machine learning
hclustWidget	shiny-oriented GUI for cluster or classifier exploration

-- K --

kmeansConverter	MLInterfaces infrastructure
kmeansI	revised MLearn interface for machine learning
knn.cv2	revised MLearn interface for machine learning
knn.cvI	revised MLearn interface for machine learning
knn2	revised MLearn interface for machine learning
knnI	revised MLearn interface for machine learning
ksvm2	revised MLearn interface for machine learning
ksvmI	revised MLearn interface for machine learning

-- L --

ldaI	revised MLearn interface for machine learning
ldaI.predParms	revised MLearn interface for machine learning
learnerIn3D	Class '"projectedLearner"'
learnerIn3D-method	Class '"projectedLearner"'
learnerSchema-class	Class "learnerSchema" - convey information on a machine learning function to the MLearn wrapper
lvq	revised MLearn interface for machine learning
lvqI	revised MLearn interface for machine learning

-- M --

macroF1	Assessing classifier performance
macroF1-method	Assessing classifier performance
macroF1-methods	Assessing classifier performance
makeClusteringSchema	MLInterfaces infrastructure
makeConfuMat	MLInterfaces infrastructure
makeLearnerSchema	revised MLearn interface for machine learning
mapPSvec	MLInterfaces infrastructure
membMat	MLInterfaces infrastructure
mkfmla	real adaboost (Friedman et al)
MLearn	revised MLearn interface for machine learning
MLearn-method	revised MLearn interface for machine learning
mlearnWidget	shiny-oriented GUI for cluster or classifier exploration
MLearn_new	revised MLearn interface for machine learning
MLIConverter.Bgbm	MLInterfaces infrastructure
MLIConverter.blackboost	MLInterfaces infrastructure
MLIConverter.dlda	MLInterfaces infrastructure
MLIConverter.knn	MLInterfaces infrastructure
MLIConverter.knncv	MLInterfaces infrastructure
MLIConverter.ksvm	MLInterfaces infrastructure
MLIConverter.ldaPredMeth	MLInterfaces infrastructure
MLIConverter.logistic	MLInterfaces infrastructure
MLIConverter.naiveBayes	MLInterfaces infrastructure
MLIConverter.nnet	MLInterfaces infrastructure
MLIConverter.plsda	MLInterfaces infrastructure
MLIConverter.RAB	MLInterfaces infrastructure
MLIConverter.randomForest	MLInterfaces infrastructure
MLIConverter.rpart	MLInterfaces infrastructure
MLIConverter.selftesting	MLInterfaces infrastructure
MLIConverter.slda	MLInterfaces infrastructure
MLIConverter.svm	MLInterfaces infrastructure
MLIConverterListEl.class	MLInterfaces infrastructure
MLIConverterPredType.class	MLInterfaces infrastructure
MLIPredicter.knn	MLInterfaces infrastructure
MLIPredicter.ksvm	MLInterfaces infrastructure
MLIPredicter.naiveBayes	MLInterfaces infrastructure
MLIPredicter.nnet	MLInterfaces infrastructure
MLIPredicter.plsda	MLInterfaces infrastructure
MLIPredicter.randomForest	MLInterfaces infrastructure
MLIPredicter.svm	MLInterfaces infrastructure
MLLabel	MLInterfaces infrastructure
MLOutput	MLInterfaces infrastructure
MLScore	MLInterfaces infrastructure

-- N --

naAs0	MLInterfaces infrastructure
naiveBayesI	revised MLearn interface for machine learning
nnetI	revised MLearn interface for machine learning
nonstandardLearnerSchema-class	Class "learnerSchema" - convey information on a machine learning function to the MLearn wrapper

-- P --

pamConverter	MLInterfaces infrastructure
pamI	revised MLearn interface for machine learning
partPlot	MLInterfaces infrastructure
planarPlot	Methods for Function planarPlot in Package 'MLInterfaces'
planarPlot-method	Methods for Function planarPlot in Package 'MLInterfaces'
planarPlot-methods	Methods for Function planarPlot in Package 'MLInterfaces'
planarPlot2	MLInterfaces infrastructure
plot	Class "varImpStruct" - collect data on variable importance from various machine learning methods
plot-method	container for clustering outputs in uniform structure
plot-method	Class '"projectedLearner"'
plot-method	Class "varImpStruct" - collect data on variable importance from various machine learning methods
plotOne	Class '"projectedLearner"'
plotOne-method	Class '"projectedLearner"'
plotXvalRDA	revised MLearn interface for machine learning
plsda2	revised MLearn interface for machine learning
plsdaI	revised MLearn interface for machine learning
plspinDF	MLInterfaces infrastructure
plspinHcube	shiny app for interactive 3D visualization of mlbench hypercube
prcomp-class	container for clustering outputs in uniform structure
prcompObj-class	container for clustering outputs in uniform structure
precision	Assessing classifier performance
precision-method	Assessing classifier performance
precision-methods	Assessing classifier performance
Predict	real adaboost (Friedman et al)
Predict-method	real adaboost (Friedman et al)
predict.classifierOutput	Predict method for 'classifierOutput' objects
predict.dlda2	MLInterfaces infrastructure
predict.gbm2	MLInterfaces infrastructure
predict.knn.cv2	MLInterfaces infrastructure
predict.knn2	MLInterfaces infrastructure
predict.lvq	MLInterfaces infrastructure
predict.RAB	MLInterfaces infrastructure
predictions	Class "classifierOutput"
predictions-method	Class "classifierOutput"
predScore	Class "classifierOutput"
predScore-method	Class "classifierOutput"
predScores	Class "classifierOutput"
predScores-method	Class "classifierOutput"
probArray	MLInterfaces infrastructure
probMat	MLInterfaces infrastructure
projectedLearner-class	Class '"projectedLearner"'
projectLearnerToGrid	create learned tesselation of feature space after PC transformation

-- Q --

qdaI	revised MLearn interface for machine learning
qualScore	MLInterfaces infrastructure

-- R --

RAB	real adaboost (Friedman et al)
rab	revised MLearn interface for machine learning
RAB4es	real adaboost (Friedman et al)
RABI	revised MLearn interface for machine learning
raboostCont-class	Class "raboostCont" ~~~
randomForestI	revised MLearn interface for machine learning
recall	Assessing classifier performance
recall-method	Assessing classifier performance
recall-methods	Assessing classifier performance
report	Class "varImpStruct" - collect data on variable importance from various machine learning methods
report-method	Class "varImpStruct" - collect data on variable importance from various machine learning methods
RObject	Class "classifierOutput"
RObject-method	Class "classifierOutput"
RObject-method	container for clustering outputs in uniform structure
rpartI	revised MLearn interface for machine learning

-- S --

se2df	MLInterfaces infrastructure
sensitivity	Assessing classifier performance
sensitivity-method	Assessing classifier performance
sensitivity-methods	Assessing classifier performance
show-method	Class "classifierOutput"
show-method	container for clustering outputs in uniform structure
show-method	Class "learnerSchema" - convey information on a machine learning function to the MLearn wrapper
show-method	Class '"projectedLearner"'
show-method	Class "raboostCont" ~~~
show-method	Class "varImpStruct" - collect data on variable importance from various machine learning methods
silhouette-class	container for clustering outputs in uniform structure
silhouetteVec	MLInterfaces infrastructure
sldaI	revised MLearn interface for machine learning
SOMBout	MLInterfaces infrastructure
somout	MLInterfaces infrastructure
specificity	Assessing classifier performance
specificity-method	Assessing classifier performance
standardMLIConverter	revised MLearn interface for machine learning
svm2	revised MLearn interface for machine learning
svmI	revised MLearn interface for machine learning

-- T --

testPredictions	Class "classifierOutput"
testPredictions-method	Class "classifierOutput"
testScores	Class "classifierOutput"
testScores-method	Class "classifierOutput"
tn	Assessing classifier performance
tn-method	Assessing classifier performance
tonp	real adaboost (Friedman et al)
tp	Assessing classifier performance
tp-method	Assessing classifier performance
trainInd	Class "classifierOutput"
trainInd-method	Class "classifierOutput"
trainPredictions	Class "classifierOutput"
trainPredictions-method	Class "classifierOutput"
trainScores	Class "classifierOutput"
trainScores-method	Class "classifierOutput"

-- V --

varImpStruct-class

Class "varImpStruct" - collect data on variable importance from various machine learning methods

-- X --

x	MLInterfaces infrastructure
xvalLoop	Cross-validation in clustered computing environments
xvalLoop-method	Cross-validation in clustered computing environments
xvalSpec	container for information specifying a cross-validated machine learning exercise
xvalSpec-class	container for information specifying a cross-validated machine learning exercise