pamr: Pam: prediction analysis for microarrays

Some functions for sample classification in microarrays

Author
T. Hastie, R. Tibshirani, Balasubramanian Narasimhan, Gil Chu
Date of publication
2014-08-27 07:27:29
Maintainer
Rob Tibshirani <tibs@stanford.edu>
License
GPL-2
Version
1.55

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