Entry: khan
Aliases: khan
Keywords: datasets
Description: Khan microarray data
URL: ../../../library/pamr/html/khan.html

Entry: pamr.adaptthresh
Aliases: pamr.adaptthresh
Keywords: 
Description: A function to adaptive choose threshold scales, for use in pamr.train
URL: ../../../library/pamr/html/pamr.adaptthresh.html

Entry: pamr.batchadjust
Aliases: pamr.batchadjust
Keywords: 
Description: A function to mean-adjust microarray data by batches
URL: ../../../library/pamr/html/pamr.batchadjust.html

Entry: pamr.confusion
Aliases: pamr.confusion
Keywords: 
Description: A function giving a table of true versus predicted values, from a nearest shrunken centroid fit.
URL: ../../../library/pamr/html/pamr.confusion.html

Entry: pamr.cv
Aliases: pamr.cv
Keywords: 
Description: A function to cross-validate the nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.cv.html

Entry: pamr.from.excel
Aliases: pamr.from.excel
Keywords: 
Description: A function to read in a text file saved from Excel
URL: ../../../library/pamr/html/pamr.from.excel.html

Entry: pamr.geneplot
Aliases: pamr.geneplot
Keywords: 
Description: A function to plot genes found by the nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.geneplot.html

Entry: pamr.internal
Aliases: pamr.internal balanced.folds softmax descendants diag.disc enlist error.bars error.nsc misreg.simple nnmiss nsc nsccv pamr.cube.root pamr.pairscore pamr.predictmany pamr.xl.compute.confusion pamr.xl.compute.cv.confusion pamr.xl.compute.offset pamr.xl.derive.adjusted.prior pamr.xl.get.default.training.parameters pamr.xl.get.offset pamr.xl.get.sample.prior pamr.xl.get.uniform.prior pamr.xl.is.a.subset pamr.xl.listgenes.compute pamr.xl.plot.test.probs.compute pamr.xl.plot.training.error.compute pamr.xl.plotcen.compute pamr.xl.plotcv.compute pamr.xl.plotcvprob.compute pamr.xl.predict.test.class pamr.xl.predict.test.class.only pamr.xl.predict.test.probs pamr.xl.process.data pamr.xl.test.data.impute pamr.xl.test.errors.compute pamr.xl.transform.class.labels pamr.xl.transform.data pamr.xl.transform.test.data permute.rows print.nsc print.nsccv roc.nsc soft.shrink softmax
Keywords: 
Description: Internal functions used by pamr
URL: ../../../library/pamr/html/pamr.internal.html

Entry: pamr.knnimpute
Aliases: pamr.knnimpute
Keywords: 
Description: A function to impute missing expression data
URL: ../../../library/pamr/html/pamr.knnimpute.html

Entry: pamr.listgenes
Aliases: pamr.listgenes
Keywords: 
Description: A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.listgenes.html

Entry: pamr.makeclasses
Aliases: pamr.makeclasses
Keywords: 
Description: A function to interactively define classes from a clustering tree
URL: ../../../library/pamr/html/pamr.makeclasses.html

Entry: pamr.menu
Aliases: pamr.menu
Keywords: 
Description: A function that interactively leads the user through a PAM analysis
URL: ../../../library/pamr/html/pamr.menu.html

Entry: pamr.plotcen
Aliases: pamr.plotcen
Keywords: 
Description: A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.plotcen.html

Entry: pamr.plotcv
Aliases: pamr.plotcv
Keywords: 
Description: A function to plot the cross-validated error curves from the nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.plotcv.html

Entry: pamr.plotcvprob
Aliases: pamr.plotcvprob
Keywords: 
Description: A function to plot the cross-validated sample probabilities from the nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.plotcvprob.html

Entry: pamr.predict
Aliases: pamr.predict
Keywords: 
Description: A function producing predicted information, from a nearest shrunken centroid fit.
URL: ../../../library/pamr/html/pamr.predict.html

Entry: pamr.to.excel
Aliases: pamr.to.excel
Keywords: 
Description: A function to write out a data object into a tab-delimited text file
URL: ../../../library/pamr/html/pamr.to.excel.html

Entry: pamr.train
Aliases: pamr.train
Keywords: 
Description: A function to train a nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.train.html
