pamr: Pam: prediction analysis for microarrays

Some functions for sample classification in microarrays

Install the latest version of this package by entering the following in R:
install.packages("pamr")
AuthorT. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu
Date of publication2014-08-27 07:27:29
MaintainerRob Tibshirani <tibs@stanford.edu>
LicenseGPL-2
Version1.55

View on CRAN

Man pages

khan: Khan microarray data

pamr.adaptthresh: A function to adaptive choose threshold scales, for use in...

pamr.batchadjust: A function to mean-adjust microarray data by batches

pamr.confusion: A function giving a table of true versus predicted values,...

pamr.confusion.survival: Compute confusin matrix from pamr survival fit

pamr.cv: A function to cross-validate the nearest shrunken centroid...

pamr.decorrelate: A function to decorrelate (adjust) the feature matrix with...

pamr.fdr: A function to estimate false discovery rates for the nearest...

pamr.from.excel: A function to read in a text file saved from Excel

pamr.geneplot: A function to plot the genes that surive the thresholding...

pamr.indeterminate: A function that takes estimate class probabilities and...

pamr.internal: Internal pamr functions

pamr.knnimpute: A function to impute missing expression data

pamr.listgenes: A function to list the genes that survive the thresholding,...

pamr.makeclasses: A function to interactively define classes from a clustering...

pamr.menu: A function that interactively leads the user through a PAM...

pamr.plotcen: A function to plot the shrunken class centroids, from the...

pamr.plotcv: A function to plot the cross-validated error curves from the...

pamr.plotcvprob: A function to plot the cross-validated sample probabilities...

pamr.plotfdr: A function to plot the FDR curve from the nearest shrunken...

pamr.plotstrata: A function to plot the survival curves in each Kaplan Meier...

pamr.plotsurvival: A function to plots Kaplan-Meier curves stratified by a group...

pamr.predict: A function giving prediction information, from a nearest...

pamr.predictmany: A function giving prediction information for many threshold...

pamr.surv.to.class2: A function to assign observations to categories, based on...

pamr.test.errors.surv.compute: A function giving a table of true versus predicted values,...

pamr.to.excel: A function to write out a data object into a tab-delimited...

pamr.train: A function to train a nearest shrunken centroid classifier

Functions

khan Man page
pamr.adaptthresh Man page
pamr.batchadjust Man page
pamr.confusion Man page
pamr.confusion.survival Man page
pamr.cube.root Man page
pamr.cv Man page
pamr.decorrelate Man page
pamr.fdr Man page
pamr.from.excel Man page
pamr.geneplot Man page
pamr.indeterminate Man page
pamr.knnimpute Man page
pamr.knnimpute.old Man page
pamr.listgenes Man page
pamr.makeclasses Man page
pamr.menu Man page
pamr.pairscore Man page
pamr.plotcen Man page
pamr.plotcv Man page
pamr.plotcvprob Man page
pamr.plotfdr Man page
pamr.plotstrata Man page
pamr.plotsurvival Man page
pamr.predict Man page
pamr.predictmany Man page
pamr.pvalue.survival Man page
pamr.score.to.class1 Man page
pamr.score.to.class2 Man page
pamr.surv.to.class2 Man page
pamr.test.errors.surv.compute Man page
pamr.to.excel Man page
pamr.train Man page
pamr.xl.compute.confusion Man page
pamr.xl.compute.cv.confusion Man page
pamr.xl.compute.offset Man page
pamr.xl.derive.adjusted.prior Man page
pamr.xl.error.trace Man page
pamr.xl.get.class.labels Man page
pamr.xl.get.class.names Man page
pamr.xl.get.default.training.parameters Man page
pamr.xl.get.number.of.classes Man page
pamr.xl.get.offset Man page
pamr.xl.get.sample.prior Man page
pamr.xl.get.soft.class.labels Man page
pamr.xl.get.threshold.range Man page
pamr.xl.get.uniform.prior Man page
pamr.xl.is.a.subset Man page
pamr.xl.listgenes.compute Man page
pamr.xl.plotcen.compute Man page
pamr.xl.plotcv.compute Man page
pamr.xl.plotcvprob.compute Man page
pamr.xl.plotsurvival Man page
pamr.xl.plotsurvival.strata Man page
pamr.xl.plotsurvival.test Man page
pamr.xl.plot.test.probs.compute Man page
pamr.xl.plot.training.error.compute Man page
pamr.xl.predict.test.class Man page
pamr.xl.predict.test.class.only Man page
pamr.xl.predict.test.probs Man page
pamr.xl.predict.test.surv.class Man page
pamr.xl.process.data Man page
pamr.xl.test.data.impute Man page
pamr.xl.test.errors.compute Man page
pamr.xl.test.errors.surv.compute Man page
pamr.xl.test.get.soft.classes Man page
pamr.xl.transform.class.labels Man page
pamr.xl.transform.data Man page
pamr.xl.transform.test.data Man page
print.nsc Man page
print.nsccv Man page
print.pamrcved Man page
print.pamrtrained Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.