Pam: prediction analysis for microarrays

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Documentation for package `pamr' version 1.27

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khan Khan microarray data
pamr.adaptthresh A function to adaptive choose threshold scales, for use in pamr.train
pamr.batchadjust A function to mean-adjust microarray data by batches
pamr.confusion A function giving a table of true versus predicted values, from a nearest shrunken centroid fit.
pamr.confusion.survival Compute confusin matrix from pamr survival fit
pamr.cv A function to cross-validate the nearest shrunken centroid classifier
pamr.decorrelate A function to decorrelate (adjust) the feature matrix with respect to some additional predictors
pamr.fdr A function to estimate false discovery rates for the nearest shrunken centroid classifier
pamr.from.excel A function to read in a text file saved from Excel
pamr.geneplot A function to plot the genes that surive the thresholding from the nearest shrunken centroid classifier
pamr.indeterminate A function that takes estimate class probabilities and produces a class prediction or indeterminate prediction
pamr.knnimpute A function to impute missing expression data
pamr.listgenes A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifier
pamr.makeclasses A function to interactively define classes from a clustering tree
pamr.menu A function that interactively leads the user through a PAM analysis
pamr.plotcen A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier
pamr.plotcv A function to plot the cross-validated error curves from the nearest shrunken centroid classifier
pamr.plotcvprob A function to plot the cross-validated sample probabilities from the nearest shrunken centroid classifier
pamr.plotfdr A function to plot the FDR curve from the nearest shrunken centroid classifier
pamr.plotstrata A function to plot the survival curves in each Kaplan Meier stratum
pamr.plotsurvival A function to plots Kaplan-Meier curves stratified by a group variable
pamr.predict A function giving prediction information, from a nearest shrunken centroid fit.
pamr.predictmany A function giving prediction information for many threshold values, from a nearest shrunken centroid fit.
pamr.surv.to.class2 A function to assign observations to categories, based on their survival times.
pamr.test.errors.surv.compute A function giving a table of true versus predicted values, from a nearest shrunken centroid fit from survival data.
pamr.to.excel A function to write out a data object into a tab-delimited text file
pamr.train A function to train a nearest shrunken centroid classifier