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\name{Dimensionality Reduction}
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\alias{MDSplot,CuffData-method}
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\alias{PCAplot,CuffData-method}
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%- Also NEED an '\alias' for EACH other topic documented here.
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Dimensionality reduction utilities
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Dimensionality reduction plots for feature selection and extraction for cummeRbund
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\S4method{MDSplot}{CuffData}(object,replicates=FALSE,logMode=TRUE,pseudocount=1.0)
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\S4method{PCAplot}{CuffData}(object,x="PC1", y="PC2",replicates=FALSE,pseudocount=1.0,scale=TRUE,...)
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%- maybe also 'usage' for other objects documented here.
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The output of class CuffData from which to draw expression estimates. (e.g. genes(cuff))
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For PCAplot, indicates which principal component is to be presented on the x-axis (e.g. "PC1","PC2","PC3", etc)
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Value added to FPKM to avoid log transformation issues.
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Logical value whether or not to use log-transformed expression estimates (default: TRUE)
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A logical value to indicate whether or not individual replicate expression estimates will be used.
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For PCAplot, a logical value passed directly to prcomp.
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Additional passthrough arguments (may not be fully implemented yet).
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These methods attempt to project a matrix of expression estimates across conditions and/or replicates onto a smaller number of dimesions for feature selection, feature extraction, and can
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also be useful for outlier detection.
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cuff<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
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p<-PCAplot(genes(cuff),x="PC2",y="PC3",replicates=TRUE)
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m<-MDSplot(genes(cuff),replicates=TRUE)
added
removed
man/dimensionality.Rd
