# Pam: prediction analysis for microarrays

## Documentation for package ‘pamr’ version 1.38.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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