Pam: prediction analysis for microarrays


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Documentation for package `pamr' version 1.12.1

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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
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