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


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Documentation for package `MLInterfaces' version 1.10.3

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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 --

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
balKfold support for cross-validatory machine learning with ExpressionSets
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
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 Methods for Function confuMat in Package `MLInterfaces'
confuMat,classifOutput-method Methods for Function confuMat in Package `MLInterfaces'
confuMat-methods Methods for Function confuMat in Package `MLInterfaces'
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) (and discrete adaboost (DAB))
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

-- 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

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

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
knn1B An interface to various machine learning methods for ExpressionSets
knn1B,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
knnB An interface to various machine learning methods for ExpressionSets
knnB,ExpressionSet,character,integer-method An interface to various machine learning methods for ExpressionSets
knnP An interface to various machine learning methods for ExpressionSets
knnP-class Class "classifOutput": container for output of classification procedures in R

-- 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
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
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

-- M --

makeCVFunc MLInterfaces infrastructure
membMat-class Class "classifOutput": container for output of classification procedures in R
mkfmla real adaboost (Friedman et al) (and discrete adaboost (DAB))
MLearn Methods for Function MLearn in Package `MLInterfaces'
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,ExpressionSet,character,numeric,ANY-method Methods for Function MLearn in Package `MLInterfaces'
MLearn,formula,ExpressionSet,character,numeric-method Methods for Function MLearn in Package `MLInterfaces'
MLearn-methods Methods for Function MLearn in Package `MLInterfaces'
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
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
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
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) (and discrete adaboost (DAB))
Predict,daboostCont-method real adaboost (Friedman et al) (and discrete adaboost (DAB))
Predict,raboostCont-method real adaboost (Friedman et al) (and discrete adaboost (DAB))
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
qualScore-class Class "classifOutput": container for output of classification procedures in R

-- R --

RAB real adaboost (Friedman et al) (and discrete adaboost (DAB))
RAB4es real adaboost (Friedman et al) (and discrete adaboost (DAB))
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
RObject An interface to various machine learning methods for ExpressionSets
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

-- S --

show,clustOutput-method Class "clustOutput" container for cluster analysis results
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
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
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

-- T --

tellMLearnMethods Methods for Function MLearn in Package `MLInterfaces'
tonp real adaboost (Friedman et al) (and discrete adaboost (DAB))
trainInds An interface to various unsupervised machine learning methods for ExpressionSets
trainInds,classifOutput-method An interface to various machine learning methods for ExpressionSets

-- 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