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


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Documentation for package ‘MLInterfaces’ version 1.14.1

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A B C D E F G H I K L M N O P Q R S T V W X

-- A --

adaI revised MLearn interface for machine learning
agnes-class Class "classifOutput": container for output of classification procedures in R
agnesB An interface to various unsupervised machine learning methods for ExpressionSets
agnesB,ExpressionSet,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets
allClass An interface to various machine learning methods for ExpressionSets
allClass,classifOutput-method An interface to various machine learning methods for ExpressionSets

-- B --

bagging-class Class "classifOutput": container for output of classification procedures in R
baggingB An interface to various machine learning methods for ExpressionSets
baggingB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
baggingI revised MLearn interface for machine learning
balKfold support for cross-validatory machine learning with ExpressionSets
balKfold.xvspec generate a partition function for cross-validation, where the partitions are approximately balanced with respect to the distribution of a response variable
bclust-class Class "clustOutput" container for cluster analysis results
bclustB An interface to various unsupervised machine learning methods for ExpressionSets
bclustB,ExpressionSet,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets

-- C --

chkMLInterfaceProc MLInterfaces infrastructure
claraB An interface to various unsupervised machine learning methods for ExpressionSets
claraB,ExpressionSet,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets
classbagg-class Class "classifOutput": container for output of classification procedures in R
classifierOutput-class Class "classifierOutput"
classifOutput Class "classifOutput": container for output of classification procedures in R
classifOutput-class Class "classifOutput": container for output of classification procedures in R
clustOutput-class Class "clustOutput" container for cluster analysis results
cmeansB An interface to various unsupervised machine learning methods for ExpressionSets
cmeansB,ExpressionSet,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets
confuMat Compute the confusion matrix for a classifier.
confuMat,classifierOutput,character-method Compute the confusion matrix for a classifier.
confuMat,classifierOutput,missing-method Compute the confusion matrix for a classifier.
confuMat,classifierOutput-method Compute the confusion matrix for a classifier.
confuMat,classifOutput,character-method Compute the confusion matrix for a classifier.
confuMat,classifOutput,missing-method Compute the confusion matrix for a classifier.
confuMat,classifOutput-method Compute the confusion matrix for a classifier.
confuMat-methods Compute the confusion matrix for a classifier.
confuMatTrain Methods for Function MLearn in Package ‘MLInterfaces’
confuMatTrain,classifOutput-method Methods for Function MLearn in Package ‘MLInterfaces’
cshell-class Class "classifOutput": container for output of classification procedures in R
cshellB An interface to various unsupervised machine learning methods for ExpressionSets
cshellB,ExpressionSet,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets
cvB An interface to various machine learning methods for ExpressionSets
cvB,ExpressionSet,character-method An interface to various machine learning methods for ExpressionSets

-- D --

DAB real adaboost (Friedman et al)
daboostCont-class Class "raboostCont" ~~~
diana-class Class "classifOutput": container for output of classification procedures in R
dianaB An interface to various unsupervised machine learning methods for ExpressionSets
dianaB,ExpressionSet,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets
dist-class Class "classifOutput": container for output of classification procedures in R
distMat An interface to various unsupervised machine learning methods for ExpressionSets
distMat,MLOutput-method An interface to various machine learning methods for ExpressionSets
dlda revised MLearn interface for machine learning
dlda2 revised MLearn interface for machine learning
dldaI revised MLearn interface for machine learning

-- E --

es2df Methods for Function MLearn in Package ‘MLInterfaces’

-- F --

fannyB An interface to various unsupervised machine learning methods for ExpressionSets
fannyB,ExpressionSet,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets
fclust-class Class "clustOutput" container for cluster analysis results
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,classifierOutput-method Class "classifierOutput"

-- G --

gbm-class Class "classifOutput": container for output of classification procedures in R
gbmB An interface to various machine learning methods for ExpressionSets
gbmB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
getGrid MLInterfaces infrastructure
getGrid,data.frame-method MLInterfaces infrastructure
getGrid,ExpressionSet-method MLInterfaces infrastructure
getVarImp Class "varImpStruct" - collect data on variable importance from various machine learning methods
getVarImp,classifierOutput,logical-method Class "varImpStruct" - collect data on variable importance from various machine learning methods
getVarImp,classifierOutput,missing-method Class "varImpStruct" - collect data on variable importance from various machine learning methods
getVarImp,classifOutput,logical-method Class "varImpStruct" - collect data on variable importance from various machine learning methods
glmI.logistic revised MLearn interface for machine learning
groupIndex-class Class "classifOutput": container for output of classification procedures in R

-- H --

hclust-class Class "clustOutput" container for cluster analysis results
hclustB An interface to various unsupervised machine learning methods for ExpressionSets
hclustB,ExpressionSet,missing,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets
hclustB,ExpressionSet,numeric,ANY-method An interface to various unsupervised machine learning methods for ExpressionSets
hclustB,ExpressionSet,numeric,missing-method An interface to various unsupervised machine learning methods for ExpressionSets

-- I --

ica-class Class "classifOutput": container for output of classification procedures in R
ipredknn-class Class "classifOutput": container for output of classification procedures in R
ipredknnB An interface to various machine learning methods for ExpressionSets
ipredknnB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
isoMDSB An interface to various unsupervised machine learning methods for ExpressionSets

-- K --

Kfold for given n, generate a K-fold partition of 1:n
kmeans-class Class "classifOutput": container for output of classification procedures in R
kmeansB An interface to various unsupervised machine learning methods for ExpressionSets
kmeansB,ExpressionSet,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets
knn.cv2 revised MLearn interface for machine learning
knn.cvI revised MLearn interface for machine learning
knn1B An interface to various machine learning methods for ExpressionSets
knn1B,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
knn2 revised MLearn interface for machine learning
knnB An interface to various machine learning methods for ExpressionSets
knnB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
knnI revised MLearn interface for machine learning
knnP An interface to various machine learning methods for ExpressionSets
knnP-class Class "classifOutput": container for output of classification procedures in R
ksvmI revised MLearn interface for machine learning

-- L --

last.warning An interface to various machine learning methods for ExpressionSets
lca-class Class "classifOutput": container for output of classification procedures in R
lcaB An interface to various machine learning methods for ExpressionSets
lcaB,ExpressionSet,numeric-method An interface to various machine learning methods for ExpressionSets
lda-class Class "classifOutput": container for output of classification procedures in R
ldaB An interface to various machine learning methods for ExpressionSets
ldaB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
ldaI revised MLearn interface for machine learning
learnerSchema-class Class "learnerSchema" - convey information on a machine learning function to the MLearn wrapper
logitboost-class Class "classifOutput": container for output of classification procedures in R
logitboostB An interface to various machine learning methods for ExpressionSets
logitboostB,ExpressionSet,character,integer,numeric-method An interface to various machine learning methods for ExpressionSets
lvq revised MLearn interface for machine learning
lvq1B An interface to various machine learning methods for ExpressionSets
lvq1B,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
lvq2B An interface to various machine learning methods for ExpressionSets
lvq2B,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
lvq3B An interface to various machine learning methods for ExpressionSets
lvq3B,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
lvqI revised MLearn interface for machine learning

-- M --

makeLearnerSchema revised MLearn interface for machine learning
membMat-class Class "classifOutput": container for output of classification procedures in R
mkfmla real adaboost (Friedman et al)
MLearn revised MLearn interface for machine learning
MLearn,formula,data.frame,character,numeric,ANY-method Methods for Function MLearn in Package ‘MLInterfaces’
MLearn,formula,data.frame,character,numeric-method Methods for Function MLearn in Package ‘MLInterfaces’
MLearn,formula,data.frame,learnerSchema,numeric,missing-method revised MLearn interface for machine learning
MLearn,formula,data.frame,learnerSchema,xvalSpec,missing-method revised MLearn interface for machine learning
MLearn,formula,ExpressionSet,character,numeric,ANY-method Methods for Function MLearn in Package ‘MLInterfaces’
MLearn,formula,ExpressionSet,character,numeric,missing-method revised MLearn interface for machine learning
MLearn,formula,ExpressionSet,character,numeric-method Methods for Function MLearn in Package ‘MLInterfaces’
MLearn,formula,ExpressionSet,learnerSchema,numeric,missing-method revised MLearn interface for machine learning
MLearn,formula,ExpressionSet,learnerSchema,xvalSpec,missing-method revised MLearn interface for machine learning
MLearn-methods Methods for Function MLearn in Package ‘MLInterfaces’
MLearn-OLD Methods for Function MLearn in Package ‘MLInterfaces’
MLearn_new revised MLearn interface for machine learning
MLLabel Class "classifOutput": container for output of classification procedures in R
MLLabel-class Class "classifOutput": container for output of classification procedures in R
MLOutput Class "classifOutput": container for output of classification procedures in R
MLOutput-class Class "classifOutput": container for output of classification procedures in R
MLScore Class "classifOutput": container for output of classification procedures in R
MLScore-class Class "classifOutput": container for output of classification procedures in R

-- N --

naiveBayes-class Class "classifOutput": container for output of classification procedures in R
naiveBayesB An interface to various machine learning methods for ExpressionSets
naiveBayesB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
naiveBayesI revised MLearn interface for machine learning
newGroupIndex MLInterfaces infrastructure
newMembMat MLInterfaces infrastructure
newPredClass MLInterfaces infrastructure
newProbArray MLInterfaces infrastructure
newProbMat MLInterfaces infrastructure
newQualScore MLInterfaces infrastructure
newSilhouetteVec MLInterfaces infrastructure
nnet.formula-class Class "classifOutput": container for output of classification procedures in R
nnetB An interface to various machine learning methods for ExpressionSets
nnetB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
nnetI revised MLearn interface for machine learning
nonstandardLearnerSchema-class Class "learnerSchema" - convey information on a machine learning function to the MLearn wrapper
nsc-class Class "classifOutput": container for output of classification procedures in R

-- O --

olvq1B An interface to various machine learning methods for ExpressionSets
olvq1B,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets

-- P --

pam-class Class "classifOutput": container for output of classification procedures in R
pamB An interface to various unsupervised machine learning methods for ExpressionSets
pamB,ExpressionSet,numeric-method An interface to various unsupervised machine learning methods for ExpressionSets
pamr-class Class "classifOutput": container for output of classification procedures in R
pamrB An interface to various machine learning methods for ExpressionSets
pamrB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
planarPlot Methods for Function planarPlot in Package ‘MLInterfaces’
planarPlot,classifOutput,data.frame,character-method Methods for Function planarPlot in Package ‘MLInterfaces’
planarPlot,classifOutput,ExpressionSet,character-method Methods for Function planarPlot in Package ‘MLInterfaces’
planarPlot-methods Methods for Function planarPlot in Package ‘MLInterfaces’
plot,varImpStruct,ANY-method Class "varImpStruct" - collect data on variable importance from various machine learning methods
plot,varImpStruct-method Class "varImpStruct" - collect data on variable importance from various machine learning methods
plotXvalRDA revised MLearn interface for machine learning
prcomp-class Class "classifOutput": container for output of classification procedures in R
predClass-class Class "classifOutput": container for output of classification procedures in R
Predict real adaboost (Friedman et al)
Predict,daboostCont-method real adaboost (Friedman et al)
Predict,raboostCont-method real adaboost (Friedman et al)
predict.knnP MLInterfaces infrastructure
predLabels An interface to various machine learning methods for ExpressionSets
predLabels,classifOutput-method An interface to various machine learning methods for ExpressionSets
predLabels,MLOutput-method An interface to various machine learning methods for ExpressionSets
predLabelsTr Methods for Function MLearn in Package ‘MLInterfaces’
predLabelsTr,classifOutput-method Methods for Function MLearn in Package ‘MLInterfaces’
print.knnP MLInterfaces infrastructure
probArray-class Class "classifOutput": container for output of classification procedures in R
probMat-class Class "classifOutput": container for output of classification procedures in R

-- Q --

qda-class Class "classifOutput": container for output of classification procedures in R
qdaB An interface to various machine learning methods for ExpressionSets
qdaB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
qdaI revised MLearn interface for machine learning
qualScore-class Class "classifOutput": container for output of classification procedures in R

-- 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" ~~~
randomForest-class Class "classifOutput": container for output of classification procedures in R
randomForestB An interface to various machine learning methods for ExpressionSets
randomForestB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
randomForestI revised MLearn interface for machine learning
rdacvI revised MLearn interface for machine learning
rdacvML revised MLearn interface for machine learning
rdaI revised MLearn interface for machine learning
rdaML revised MLearn interface for machine learning
report Class "varImpStruct" - collect data on variable importance from various machine learning methods
report,varImpStruct-method Class "varImpStruct" - collect data on variable importance from various machine learning methods
RObject An interface to various machine learning methods for ExpressionSets
RObject,classifierOutput-method Class "classifierOutput"
RObject,MLOutput-method An interface to various machine learning methods for ExpressionSets
rpart-class Class "classifOutput": container for output of classification procedures in R
rpartB An interface to various machine learning methods for ExpressionSets
rpartB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
rpartI revised MLearn interface for machine learning

-- S --

show,classifierOutput-method Class "classifierOutput"
show,clustOutput-method Class "clustOutput" container for cluster analysis results
show,learnerSchema-method Class "learnerSchema" - convey information on a machine learning function to the MLearn wrapper
show,membMat-method An interface to various machine learning methods for ExpressionSets
show,MLOutput-method An interface to various machine learning methods for ExpressionSets
show,probArray-method An interface to various machine learning methods for ExpressionSets
show,probMat-method An interface to various machine learning methods for ExpressionSets
show,qualScore-method An interface to various machine learning methods for ExpressionSets
show,raboostCont-method Class "raboostCont" ~~~
show,silhouetteVec-method An interface to various machine learning methods for ExpressionSets
show,SOMBout-method An interface to self-organizing map methods for ExpressionSets
show,somout-method An interface to self-organizing map methods for ExpressionSets
show,varImpStruct-method Class "varImpStruct" - collect data on variable importance from various machine learning methods
silhouetteB An interface to various unsupervised machine learning methods for ExpressionSets
silhouetteB,classifOutput-method Class "classifOutput": container for output of classification procedures in R
silhouetteB,clustOutput-method Class "clustOutput" container for cluster analysis results
silhouetteVec-class Class "classifOutput": container for output of classification procedures in R
slda-class Class "classifOutput": container for output of classification procedures in R
sldaB An interface to various machine learning methods for ExpressionSets
sldaB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
sldaI revised MLearn interface for machine learning
SOMB An interface to self-organizing map methods for ExpressionSets
somB An interface to self-organizing map methods for ExpressionSets
SOMB,ExpressionSet,character-method An interface to self-organizing map methods for ExpressionSets
somB,ExpressionSet,character-method An interface to self-organizing map methods for ExpressionSets
SOMBout-class Class "classifOutput": container for output of classification procedures in R
somout-class An interface to self-organizing map methods for ExpressionSets
standardMLIConverter revised MLearn interface for machine learning
stat.diag.daB An interface to various machine learning methods for ExpressionSets
stat.diag.daB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
svm-class Class "classifOutput": container for output of classification procedures in R
svmB An interface to various machine learning methods for ExpressionSets
svmB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
svmI revised MLearn interface for machine learning

-- T --

tellMLearnMethods Methods for Function MLearn in Package ‘MLInterfaces’
testPredictions Class "classifierOutput"
testPredictions,classifierOutput-method Class "classifierOutput"
testScores Class "classifierOutput"
testScores,classifierOutput-method Class "classifierOutput"
tonp real adaboost (Friedman et al)
trainInds An interface to various unsupervised machine learning methods for ExpressionSets
trainInds,classifOutput-method An interface to various machine learning methods for ExpressionSets
trainPredictions Class "classifierOutput"
trainPredictions,classifierOutput-method Class "classifierOutput"

-- V --

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

-- W --

wrapClust MLInterfaces infrastructure

-- X --

xval support for cross-validatory machine learning with ExpressionSets
xval,ExpressionSet,character,genericFunction,character,integer-method support for cross-validatory machine learning with ExpressionSets
xval,ExpressionSet,character,genericFunction,character,missing-method support for cross-validatory machine learning with ExpressionSets
xval,ExpressionSet,character,nonstandardGeneric,character,integer-method support for cross-validatory machine learning with ExpressionSets
xval,ExpressionSet,character,nonstandardGeneric,character,missing-method support for cross-validatory machine learning with ExpressionSets
xval-methods support for cross-validatory machine learning with ExpressionSets
xvalLoop Cross-validation in clustered computing environments
xvalLoop,ANY-method Cross-validation in clustered computing environments
xvalLoop-methods Cross-validation in clustered computing environments
xvalML support for cross-validatory machine learning with ExpressionSets
xvalML,formula,ExpressionSet,character,character,missing,missing,missing,function,missing,missing,missing-method support for cross-validatory machine learning with ExpressionSets
xvalML,formula,ExpressionSet,character,character,missing,missing,missing,function,numeric,missing,missing-method support for cross-validatory machine learning with ExpressionSets
xvalML,formula,ExpressionSet,character,character,missing,missing,missing,missing,missing,missing,missing-method support for cross-validatory machine learning with ExpressionSets
xvalML,formula,ExpressionSet,character,character,missing,missing,missing,missing,missing,missing-method support for cross-validatory machine learning with ExpressionSets
xvalML,formula,ExpressionSet,character,character,missing-method support for cross-validatory machine learning with ExpressionSets
xvalML,formula,ExpressionSet,character,character,numeric,ANY,ANY,ANY,ANY,ANY,ANY-method support for cross-validatory machine learning with ExpressionSets
xvalML,formula,ExpressionSet,character,character,numeric,ANY,ANY,ANY,ANY,ANY-method support for cross-validatory machine learning with ExpressionSets
xvalML,formula,ExpressionSet,character,character,numeric-method support for cross-validatory machine learning with ExpressionSets
xvalSpec container for information specifying a cross-validated machine learning exercise
xvalSpec-class container for information specifying a cross-validated machine learning exercise