# pamr v1.56

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## Pam: Prediction Analysis for Microarrays

Some functions for sample classification in microarrays.

## Functions in pamr

 Name Description pamr.confusion.survival Compute confusin matrix from pamr survival fit pamr.fdr A function to estimate false discovery rates for the nearest shrunken centroid classifier pamr.cv A function to cross-validate 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.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 khan Khan microarray data pamr.batchadjust A function to mean-adjust microarray data by batches pamr.geneplot A function to plot the genes that surive the thresholding from the nearest shrunken centroid classifier pamr.adaptthresh A function to adaptive choose threshold scales, for use in pamr.train pamr.train A function to train a nearest shrunken centroid classifier pamr.confusion A function giving a table of true versus predicted values, from a nearest shrunken centroid fit. pamr.indeterminate A function that takes estimate class probabilities and produces a class prediction or indeterminate prediction 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.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-internal Internal pamr functions pamr.listgenes A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifier pamr.surv.to.class2 A function to assign observations to categories, based on their survival times. pamr.predict A function giving prediction information, from a nearest shrunken centroid fit. 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.predictmany A function giving prediction information for many threshold values, from a nearest shrunken centroid fit. pamr.decorrelate A function to decorrelate (adjust) the feature matrix with respect to some additional predictors No Results!