pamr

Khan microarray data

A function to adaptive choose threshold scales, for use in pamr.train

A function to mean-adjust microarray data by batches

A function giving a table of true versus predicted values, from a nearest shrunken centroid fit.

Compute confusin matrix from pamr survival fit

A function to cross-validate the nearest shrunken centroid classifier

A function to decorrelate (adjust) the feature matrix with respect to some additional predictors

A function to estimate false discovery rates for the nearest shrunken centroid classifier

A function to plot the genes that surive the thresholding from the nearest shrunken centroid classifier

A function that takes estimate class probabilities and produces a class prediction or indeterminate prediction

Internal pamr functions

A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifier

A function to interactively define classes from a clustering tree

A function that interactively leads the user through a PAM analysis

A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier

A function to plot the cross-validated error curves from the nearest shrunken centroid classifier

A function to plot the cross-validated sample probabilities from the nearest shrunken centroid classifier

A function to plot the FDR curve from the nearest shrunken centroid classifier

A function to plot the survival curves in each Kaplan Meier stratum

A function to plots Kaplan-Meier curves stratified by a group variable

A function giving prediction information, from a nearest shrunken centroid fit.

A function giving prediction information for many threshold values, from a nearest shrunken centroid fit.

A function to assign observations to categories, based on their survival times.

A function giving a table of true versus predicted values, from a nearest shrunken centroid fit from survival data.

A function to train a nearest shrunken centroid classifier