# Machine Learning Interface for RNA-Seq Data

## Documentation for package ‘MLSeq’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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