Package: pamr 1.57

pamr: Pam: Prediction Analysis for Microarrays

Some functions for sample classification in microarrays.

Authors:Trevor Hastie [aut], Rob Tibshirani [aut], Balasubramanian Narasimhan [aut, cre], Gilbert Chu [aut]

pamr_1.57.tar.gz
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pamr_1.57.tgz(r-4.4-any)pamr_1.57.tgz(r-4.3-any)
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pamr_1.57.tgz(r-4.4-emscripten)pamr_1.57.tgz(r-4.3-emscripten)
pamr.pdf |pamr.html✨
pamr/json (API)

# Install 'pamr' in R:
install.packages('pamr', repos = c('https://bnaras.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bnaras/pamr/issues

Datasets:
  • khan - Khan microarray data

On CRAN:

6.87 score 14 packages 241 scripts 7.3k downloads 23 exports 4 dependencies

Last updated 5 months agofrom:768e5af7b7. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 29 2024
R-4.5-winOKOct 29 2024
R-4.5-linuxOKOct 29 2024
R-4.4-winOKOct 29 2024
R-4.4-macOKOct 29 2024
R-4.3-winOKOct 29 2024
R-4.3-macOKOct 29 2024

Exports:pamr.adaptthreshpamr.batchadjustpamr.confusionpamr.confusion.survivalpamr.cvpamr.decorrelatepamr.fdrpamr.geneplotpamr.indeterminatepamr.listgenespamr.makeclassespamr.menupamr.plotcenpamr.plotcvpamr.plotcvprobpamr.plotfdrpamr.plotstratapamr.plotsurvivalpamr.predictpamr.predictmanypamr.surv.to.class2pamr.test.errors.surv.computepamr.train

Dependencies:clusterlatticeMatrixsurvival

Readme and manuals

Help Manual

Help pageTopics
Khan microarray datakhan
A function to adaptive choose threshold scales, for use in pamr.trainpamr.adaptthresh
A function to mean-adjust microarray data by batchespamr.batchadjust
A function giving a table of true versus predicted values, from a nearest shrunken centroid fit.pamr.confusion
Compute confusin matrix from pamr survival fitpamr.confusion.survival
A function to cross-validate the nearest shrunken centroid classifierpamr.cv
A function to decorrelate (adjust) the feature matrix with respect to some additional predictorspamr.decorrelate
A function to estimate false discovery rates for the nearest shrunken centroid classifierpamr.fdr
A function to plot the genes that surive the thresholding from the nearest shrunken centroid classifierpamr.geneplot
A function that takes estimate class probabilities and produces a class prediction or indeterminate predictionpamr.indeterminate
A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifierpamr.listgenes
A function to interactively define classes from a clustering treepamr.makeclasses
A function that interactively leads the user through a PAM analysispamr.menu
A function to plot the shrunken class centroids, from the nearest shrunken centroid classifierpamr.plotcen
A function to plot the cross-validated error curves from the nearest shrunken centroid classifierpamr.plotcv
A function to plot the cross-validated sample probabilities from the nearest shrunken centroid classifierpamr.plotcvprob
A function to plot the FDR curve from the nearest shrunken centroid classifierpamr.plotfdr
A function to plot the survival curves in each Kaplan Meier stratumpamr.plotstrata
A function to plots Kaplan-Meier curves stratified by a group variablepamr.plotsurvival
A function giving prediction information, from a nearest shrunken centroid fit.pamr.predict
A function giving prediction information for many threshold values, from a nearest shrunken centroid fit.pamr.predictmany
A function to assign observations to categories, based on their survival times.pamr.surv.to.class2
A function giving a table of true versus predicted values, from a nearest shrunken centroid fit from survival data.pamr.test.errors.surv.compute
A function to train a nearest shrunken centroid classifierpamr.train