pamr: Pam: prediction analysis for microarrays

Some functions for sample classification in microarrays

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

Files in this package

pamr
pamr/src
pamr/src/knnimpute.f
pamr/NAMESPACE
pamr/data
pamr/data/khan.rda
pamr/data/datalist
pamr/R
pamr/R/pamr.plotcvprob.R pamr/R/print.pamrcved.R pamr/R/pamr.listgenes.R pamr/R/pamr.plotcv.R pamr/R/pamr.decorrelate.R pamr/R/pamr.predictmany.R pamr/R/diag.disc.R pamr/R/print.nsccv.R pamr/R/pamr.xlfuns.R pamr/R/pamr.indeterminate.R pamr/R/allknnimp.R pamr/R/pamr.menu.R pamr/R/error.nsc.R pamr/R/print.pamrtrained.R pamr/R/softshrink.R pamr/R/pamr.plotcen.R pamr/R/print.nsc.R pamr/R/pamr.plotfdr.R pamr/R/pamr.geneplot.R pamr/R/pamr.predict.R pamr/R/nsc.R pamr/R/pamr.makeclasses.R pamr/R/pamr.cv.R pamr/R/permute.rows.R pamr/R/pamr.pairscore.R pamr/R/pamr.to.excel.R pamr/R/pamr.adaptthresh.R pamr/R/pamr.train.R pamr/R/nsccv.R pamr/R/which.is.max.R pamr/R/pamr.plotstrata.R pamr/R/pamr.from.excel.R pamr/R/descendants.R pamr/R/balanced.folds.R pamr/R/pamr.knnimpute.R pamr/R/pamr.survfuns.R pamr/R/pamr.confusion.R pamr/R/enlist.R pamr/R/roc.R pamr/R/pamr.cube.root.R pamr/R/pamr.fdr.R pamr/R/softmax.R
pamr/MD5
pamr/DESCRIPTION
pamr/man
pamr/man/pamr.to.excel.Rd pamr/man/pamr.predictmany.Rd pamr/man/pamr.confusion.survival.Rd pamr/man/pamr.knnimpute.Rd pamr/man/pamr.predict.Rd pamr/man/pamr.decorrelate.Rd pamr/man/pamr.surv.to.class2.Rd pamr/man/khan.Rd pamr/man/pamr.menu.Rd pamr/man/pamr.plotsurvival.Rd pamr/man/pamr.test.errors.surv.compute.Rd pamr/man/pamr.from.excel.Rd pamr/man/pamr.plotcen.Rd pamr/man/pamr.confusion.Rd pamr/man/pamr.internal.Rd pamr/man/pamr.plotcvprob.Rd pamr/man/pamr.plotfdr.Rd pamr/man/pamr.adaptthresh.Rd pamr/man/pamr.geneplot.Rd pamr/man/pamr.batchadjust.Rd pamr/man/pamr.plotcv.Rd pamr/man/pamr.listgenes.Rd pamr/man/pamr.makeclasses.Rd pamr/man/pamr.train.Rd pamr/man/pamr.fdr.Rd pamr/man/pamr.plotstrata.Rd pamr/man/pamr.cv.Rd pamr/man/pamr.indeterminate.Rd
pamr/INDEX

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

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