Machine Learning Interface for RNA-Seq Data

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Documentation for package ‘MLSeq’ version 2.27.0

• 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