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pamr (version 1.54.1)

Pam: prediction analysis for microarrays

Description

Some functions for sample classification in microarrays

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Version

Install

install.packages('pamr')

Monthly Downloads

10,686

Version

1.54.1

License

GPL-2

Maintainer

ORPHANED

Last Published

July 24th, 2013

Functions in pamr (1.54.1)

pamr.makeclasses

A function to interactively define classes from a clustering tree
pamr.batchadjust

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

A function to plot the FDR curve from the nearest shrunken centroid classifier
khan

Khan microarray data
pamr.plotcv

A function to plot the cross-validated error curves from the nearest shrunken centroid classifier
pamr.plotcen

A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier
pamr.plotstrata

A function to plot the survival curves in each Kaplan Meier stratum
order.restricted

Compute the order of a vector subject to restrictions.
pamr.confusion.survival

Compute confusin matrix from pamr survival fit
pamr.indeterminate

A function that takes estimate class probabilities and produces a class prediction or indeterminate prediction
pamr.predict

A function giving prediction information, from a nearest shrunken centroid fit.
pamr.from.excel

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

A function giving prediction information for many threshold values, from a nearest shrunken centroid fit.
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-internal

Internal pamr functions
pamr.listgenes

A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifier
pamr.to.excel

A function to write out a data object into a tab-delimited text file
pamr.plotcvprob

A function to plot the cross-validated sample probabilities from the nearest shrunken centroid classifier
pamr.menu

A function that interactively leads the user through a PAM analysis
pamr.fdr

A function to estimate false discovery rates for the nearest shrunken centroid classifier
pamr.geneplot

A function to plot the genes that surive the thresholding from the nearest shrunken centroid classifier
pamr.plotsurvival

A function to plots Kaplan-Meier curves stratified by a group variable
pamr.confusion

A function giving a table of true versus predicted values, from a nearest shrunken centroid fit.
pamr.surv.to.class2

A function to assign observations to categories, based on their survival times.
pamr.knnimpute

A function to impute missing expression data
pamr.adaptthresh

A function to adaptive choose threshold scales, for use in pamr.train
pamr.decorrelate

A function to decorrelate (adjust) the feature matrix with respect to some additional predictors
pamr.train

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

A function to cross-validate the nearest shrunken centroid classifier