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.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-internal
Aliases: pamr.pairscore pamr.pvalue.survival pamr.score.to.class1 pamr.score.to.class2 pamr.knnimpute.old pamr.cube.root
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.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
