# Pam: prediction analysis for microarrays

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

balanced.folds | Internal functions used by pamr
descendants | Internal functions used by pamr
diag.disc | Internal functions used by pamr
enlist | Internal functions used by pamr
error.bars | Internal functions used by pamr
error.nsc | Internal functions used by pamr
khan | Khan microarray data
khanEset | Khan microarray data
misreg.simple | Internal functions used by pamr
nnmiss | Internal functions used by pamr
nsc | Internal functions used by pamr
nsccv | Internal functions used by pamr
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.cube.root | Internal functions used by pamr
pamr.cv | A function to cross-validate 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 genes found by the nearest shrunken centroid classifier
pamr.internal | Internal functions used by pamr
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.pairscore | Internal functions used by pamr
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.predict | A function producing predicted information, from a nearest shrunken centroid fit.
pamr.predictmany | Internal functions used by pamr
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
pamr.xl.compute.confusion | Internal functions used by pamr
pamr.xl.compute.cv.confusion | Internal functions used by pamr
pamr.xl.compute.offset | Internal functions used by pamr
pamr.xl.derive.adjusted.prior | Internal functions used by pamr
pamr.xl.get.default.training.parameters | Internal functions used by pamr
pamr.xl.get.offset | Internal functions used by pamr
pamr.xl.get.sample.prior | Internal functions used by pamr
pamr.xl.get.uniform.prior | Internal functions used by pamr
pamr.xl.is.a.subset | Internal functions used by pamr
pamr.xl.listgenes.compute | Internal functions used by pamr
pamr.xl.plot.test.probs.compute | Internal functions used by pamr
pamr.xl.plot.training.error.compute | Internal functions used by pamr
pamr.xl.plotcen.compute | Internal functions used by pamr
pamr.xl.plotcv.compute | Internal functions used by pamr
pamr.xl.plotcvprob.compute | Internal functions used by pamr
pamr.xl.predict.test.class | Internal functions used by pamr
pamr.xl.predict.test.probs | Internal functions used by pamr
pamr.xl.process.data | Internal functions used by pamr
pamr.xl.test.data.impute | Internal functions used by pamr
pamr.xl.test.errors.compute | Internal functions used by pamr
pamr.xl.transform.class.labels | Internal functions used by pamr
pamr.xl.transform.data | Internal functions used by pamr
pamr.xl.transform.test.data | Internal functions used by pamr
permute.rows | Internal functions used by pamr
print.nsc | Internal functions used by pamr
print.nsccv | Internal functions used by pamr
roc.nsc | Internal functions used by pamr
soft.shrink | Internal functions used by pamr
softmax | Internal functions used by pamr
softmax} | Internal functions used by pamr