RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (1.56.1) of this package.
Take me there.
pamr (version 1.56)
Pam: Prediction Analysis for Microarrays
Description
Some functions for sample classification in microarrays.
Copy Link
Copy
Link to current version
Version
Version
1.56.1
1.56
1.55
1.54.1
1.53
1.51.1
1.51
1.50
1.48.0
1.47
1.46.0
1.44.0
1.42.0
1.33
1.31
1.29
1.28
1.27
1.25
1.24
1.23
1.22
1.21
1.12.1
Down Chevron
Install
install.packages('pamr')
Monthly Downloads
4,729
Version
1.56
License
GPL-2
Maintainer
Rob Tibshirani
Last Published
February 1st, 2019
Functions in pamr (1.56)
Search functions
pamr.confusion.survival
Compute confusin matrix from pamr survival fit
pamr.fdr
A function to estimate false discovery rates for the nearest shrunken centroid classifier
pamr.cv
A function to cross-validate the nearest shrunken centroid classifier
pamr.makeclasses
A function to interactively define classes from a clustering tree
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.plotfdr
A function to plot the FDR curve from the nearest shrunken centroid classifier
khan
Khan microarray data
pamr.batchadjust
A function to mean-adjust microarray data by batches
pamr.geneplot
A function to plot the genes that surive the thresholding from the nearest shrunken centroid classifier
pamr.adaptthresh
A function to adaptive choose threshold scales, for use in pamr.train
pamr.train
A function to train a nearest shrunken centroid classifier
pamr.confusion
A function giving a table of true versus predicted values, from a nearest shrunken centroid fit.
pamr.indeterminate
A function that takes estimate class probabilities and produces a class prediction or indeterminate prediction
pamr.plotstrata
A function to plot the survival curves in each Kaplan Meier stratum
pamr.plotsurvival
A function to plots Kaplan-Meier curves stratified by a group variable
pamr.plotcen
A function to plot the shrunken class centroids, from the nearest shrunken centroid classifier
pamr.plotcv
A function to plot the cross-validated error curves from the nearest shrunken centroid classifier
pamr-internal
Internal pamr functions
pamr.listgenes
A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifier
pamr.surv.to.class2
A function to assign observations to categories, based on their survival times.
pamr.predict
A function giving prediction information, 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.predictmany
A function giving prediction information for many threshold values, from a nearest shrunken centroid fit.
pamr.decorrelate
A function to decorrelate (adjust) the feature matrix with respect to some additional predictors