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pamr (version 1.55)
Pam: prediction analysis for microarrays
Description
Some functions for sample classification in microarrays
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Install
install.packages('pamr')
Monthly Downloads
4,729
Version
1.55
License
GPL-2
Maintainer
Rob Tibshirani
Last Published
August 27th, 2014
Functions in pamr (1.55)
Search functions
pamr.test.errors.surv.compute
A function giving a table of true versus predicted values, from a nearest shrunken centroid fit from survival data.
pamr.plotfdr
A function to plot the FDR curve from the nearest shrunken centroid classifier
pamr.geneplot
A function to plot the genes that surive the thresholding from the nearest shrunken centroid classifier
pamr.decorrelate
A function to decorrelate (adjust) the feature matrix with respect to some additional predictors
pamr.listgenes
A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifier
pamr-internal
Internal pamr functions
pamr.fdr
A function to estimate false discovery rates for the nearest shrunken centroid classifier
pamr.menu
A function that interactively leads the user through a PAM analysis
pamr.batchadjust
A function to mean-adjust microarray data by batches
pamr.train
A function to train a nearest shrunken centroid classifier
pamr.plotcv
A function to plot the cross-validated error curves from the nearest shrunken centroid classifier
pamr.indeterminate
A function that takes estimate class probabilities and produces a class prediction or indeterminate prediction
pamr.from.excel
A function to read in a text file saved from Excel
pamr.to.excel
A function to write out a data object into a tab-delimited text file
pamr.confusion
A function giving a table of true versus predicted values, from a nearest shrunken centroid fit.
khan
Khan microarray data
pamr.predict
A function giving prediction information, from a nearest shrunken centroid fit.
pamr.surv.to.class2
A function to assign observations to categories, based on their survival times.
pamr.cv
A function to cross-validate the nearest shrunken centroid classifier
pamr.plotcvprob
A function to plot the cross-validated sample probabilities from the nearest shrunken centroid classifier
pamr.plotsurvival
A function to plots Kaplan-Meier curves stratified by a group variable
pamr.makeclasses
A function to interactively define classes from a clustering tree
pamr.knnimpute
A function to impute missing expression data
pamr.plotstrata
A function to plot the survival curves in each Kaplan Meier stratum
pamr.predictmany
A function giving prediction information for many threshold values, from a nearest shrunken centroid fit.
pamr.adaptthresh
A function to adaptive choose threshold scales, for use in pamr.train
pamr.plotcen
A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier
pamr.confusion.survival
Compute confusin matrix from pamr survival fit