# pamr

Prediction Analysis of Microarrays

Prediction Analysis of Microarrays

`install.packages('pamr')`

6,433

1.57

GPL-2

July 1st, 2024

pamr.plotfdr

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

pamr.surv.to.class2

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

pamr.train

A function to train a nearest shrunken centroid classifier

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.indeterminate

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

pamr.listgenes

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

pamr.predict

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

pamr.predictmany

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

pamr.confusion

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

khan

Khan microarray data

pamr.fdr

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

pamr.decorrelate

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

pamr.confusion.survival

Compute confusin matrix from pamr survival fit

pamr.geneplot

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

pamr.batchadjust

A function to mean-adjust microarray data by batches

pamr.adaptthresh

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

pamr.cv

A function to cross-validate the nearest shrunken centroid classifier

pamr.plotstrata

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

pamr.menu

A function that interactively leads the user through a PAM analysis

pamr.plotcvprob

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

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.makeclasses

A function to interactively define classes from a clustering tree

pamr.plotsurvival

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

pamr-package

Prediction Analysis of Microarrays