MLSeq-package | Machine learning interface for RNA-Seq data |
Available-classifiers | Available classification/regression methods in 'MLSeq' |
availableMethods | Available classification/regression methods in 'MLSeq' |
cervical | Cervical cancer data |
classify | Fitting classification models to sequencing data |
confusionMat | Accessors for the 'confusionMat' slot. |
confusionMat-method | Accessors for the 'confusionMat' slot. |
control | Accessors for the 'control' slot. |
control-method | Accessors for the 'control' slot. |
control<- | Accessors for the 'control' slot. |
control<--method | Accessors for the 'control' slot. |
discrete.train-class | 'discrete.train' object |
discreteControl | Define controlling parameters for discrete classifiers (NBLDA and PLDA) |
input | Accessors for the 'inputObject' slot of an 'MLSeq' object |
input-method | Accessors for the 'inputObject' slot of an 'MLSeq' object |
isModified | Checks if MLSeq object is updated/modified or not. |
isModified-method | Checks if MLSeq object is updated/modified or not. |
isModified<- | Checks if MLSeq object is updated/modified or not. |
isModified<--method | Checks if MLSeq object is updated/modified or not. |
isUpdated | Checks if MLSeq object is updated/modified or not. |
isUpdated-method | Checks if MLSeq object is updated/modified or not. |
isUpdated<- | Checks if MLSeq object is updated/modified or not. |
isUpdated<--method | Checks if MLSeq object is updated/modified or not. |
metaData | Accessors for the 'metaData' slot of an 'MLSeq' object |
metaData-method | Accessors for the 'metaData' slot of an 'MLSeq' object |
method | Accessors for the 'method'. |
method-method | Accessors for the 'method'. |
method<- | Accessors for the 'method'. |
method<--method | Accessors for the 'method'. |
MLSeq-class | 'MLSeq' object |
MLSeqMetaData-class | 'MLSeqMetaData' object |
MLSeqModelInfo-class | 'MLSeqModelInfo' object |
modelInfo | Accessors for the 'modelInfo' slot of an 'MLSeq' object |
modelInfo-method | Accessors for the 'modelInfo' slot of an 'MLSeq' object |
normalization | Accessors for the 'normalization' slot. |
normalization-method | Accessors for the 'normalization' slot. |
normalization<- | Accessors for the 'normalization' slot. |
normalization<--method | Accessors for the 'normalization' slot. |
plot | Plot accuracy results from 'MLSeq' object |
plot-method | Plot accuracy results from 'MLSeq' object |
plot.MLSeq | Plot accuracy results from 'MLSeq' object |
predict | Extract predictions from 'classify()' object |
predict-method | Extract predictions from 'classify()' object |
predict.MLSeq | Extract predictions from 'classify()' object |
predictClassify | Extract predictions from 'classify()' object |
preProcessing | Accessors for the 'preProcessing' slot of an 'MLSeq' object |
preProcessing-method | Accessors for the 'preProcessing' slot of an 'MLSeq' object |
preProcessing<- | Accessors for the 'preProcessing' slot of an 'MLSeq' object |
preProcessing<--method | Accessors for the 'preProcessing' slot of an 'MLSeq' object |
print-method | Print method for confusion matrix |
print.confMat | Print method for confusion matrix |
printAvailableMethods | Available classification/regression methods in 'MLSeq' |
ref | Accessors for the 'ref' slot. |
ref-method | Accessors for the 'ref' slot. |
ref<- | Accessors for the 'ref' slot. |
ref<--method | Accessors for the 'ref' slot. |
selectedGenes | Accessors for the 'selectedGenes'. |
selectedGenes-method | Accessors for the 'selectedGenes'. |
show | Show method for MLSeq objects |
show-method | Show method for MLSeq objects |
show.MLSeq | Show method for MLSeq objects |
trained | Accessors for the 'trainedModel' slot. |
trained-method | Accessors for the 'trainedModel' slot. |
trainParameters | Accessors for the 'trainParameters' slot. |
trainParameters-method | Accessors for the 'trainParameters' slot. |
transformation | Accessors for the 'transformation' slot. |
transformation-method | Accessors for the 'transformation' slot. |
update | Update 'MLSeq' objects returnd from 'classify()' |
update-method | Update 'MLSeq' objects returnd from 'classify()' |
update.MLSeq | Update 'MLSeq' objects returnd from 'classify()' |
voom.train-class | 'voom.train' object |
voomControl | Define controlling parameters for voom-based classifiers |