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.confusion.survival
Aliases: pamr.confusion.survival
Keywords: 
Description: Compute confusin matrix from pamr survival fit
URL: ../../../library/pamr/html/pamr.confusion.survival.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.decorrelate
Aliases: pamr.decorrelate
Keywords: 
Description: A function to decorrelate (adjust) the feature matrix with respect to some additional predictors
URL: ../../../library/pamr/html/pamr.decorrelate.html

Entry: pamr.fdr
Aliases: pamr.fdr
Keywords: 
Description: A function to estimate false discovery rates for the nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.fdr.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 the genes that surive the thresholding from the nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.geneplot.html

Entry: pamr.indeterminate
Aliases: pamr.indeterminate
Keywords: 
Description: A function that takes estimate class probabilities and produces a class prediction or indeterminate prediction
URL: ../../../library/pamr/html/pamr.indeterminate.html

Entry: pamr-internal
Aliases: pamr.cube.root pamr.knnimpute.old pamr.pairscore pamr.pvalue.survival pamr.score.to.class1 pamr.score.to.class2 print.nsc print.nsccv print.pamrcved print.pamrtrained pamr.xl.compute.offset pamr.xl.error.trace pamr.xl.get.offset pamr.xl.derive.adjusted.prior pamr.xl.get.default.training.parameters pamr.xl.get.uniform.prior pamr.xl.get.sample.prior pamr.xl.get.class.names pamr.xl.get.class.labels pamr.xl.get.number.of.classes pamr.xl.process.data pamr.xl.compute.cv.confusion pamr.xl.compute.confusion 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.test.data.impute pamr.xl.test.errors.surv.compute pamr.xl.test.errors.compute pamr.xl.transform.class.labels pamr.xl.transform.data pamr.xl.transform.test.data pamr.xl.plotsurvival pamr.xl.plotsurvival.test pamr.xl.predict.test.surv.class pamr.xl.plotsurvival.strata pamr.xl.test.get.soft.classes pamr.xl.get.threshold.range pamr.xl.get.soft.class.labels
Keywords: internal
Description: Internal pamr functions
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.plotfdr
Aliases: pamr.plotfdr
Keywords: 
Description: A function to plot the FDR curve from the nearest shrunken centroid classifier
URL: ../../../library/pamr/html/pamr.plotfdr.html

Entry: pamr.plotstrata
Aliases: pamr.plotstrata
Keywords: 
Description: A function to plot the survival curves in each Kaplan Meier stratum
URL: ../../../library/pamr/html/pamr.plotstrata.html

Entry: pamr.plotsurvival
Aliases: pamr.plotsurvival
Keywords: 
Description: A function to plots Kaplan-Meier curves stratified by a group variable
URL: ../../../library/pamr/html/pamr.plotsurvival.html

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

Entry: pamr.predictmany
Aliases: pamr.predictmany
Keywords: 
Description: A function giving prediction information for many threshold values, from a nearest shrunken centroid fit.
URL: ../../../library/pamr/html/pamr.predictmany.html

Entry: pamr.surv.to.class2
Aliases: pamr.surv.to.class2
Keywords: 
Description: A function to assign observations to categories, based on their survival times.
URL: ../../../library/pamr/html/pamr.surv.to.class2.html

Entry: pamr.test.errors.surv.compute
Aliases: pamr.test.errors.surv.compute
Keywords: 
Description: A function giving a table of true versus predicted values, from a nearest shrunken centroid fit from survival data.
URL: ../../../library/pamr/html/pamr.test.errors.surv.compute.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
