\HeaderA{pamr-internal}{Internal pamr functions}{pamr.Rdash.internal}
\aliasA{pamr.cube.root}{pamr-internal}{pamr.cube.root}
\aliasA{pamr.knnimpute.old}{pamr-internal}{pamr.knnimpute.old}
\aliasA{pamr.pairscore}{pamr-internal}{pamr.pairscore}
\aliasA{pamr.pvalue.survival}{pamr-internal}{pamr.pvalue.survival}
\aliasA{pamr.score.to.class1}{pamr-internal}{pamr.score.to.class1}
\aliasA{pamr.score.to.class2}{pamr-internal}{pamr.score.to.class2}
\aliasA{pamr.xl.compute.confusion}{pamr-internal}{pamr.xl.compute.confusion}
\aliasA{pamr.xl.compute.cv.confusion}{pamr-internal}{pamr.xl.compute.cv.confusion}
\aliasA{pamr.xl.compute.offset}{pamr-internal}{pamr.xl.compute.offset}
\aliasA{pamr.xl.derive.adjusted.prior}{pamr-internal}{pamr.xl.derive.adjusted.prior}
\aliasA{pamr.xl.error.trace}{pamr-internal}{pamr.xl.error.trace}
\aliasA{pamr.xl.get.class.labels}{pamr-internal}{pamr.xl.get.class.labels}
\aliasA{pamr.xl.get.class.names}{pamr-internal}{pamr.xl.get.class.names}
\aliasA{pamr.xl.get.default.training.parameters}{pamr-internal}{pamr.xl.get.default.training.parameters}
\aliasA{pamr.xl.get.number.of.classes}{pamr-internal}{pamr.xl.get.number.of.classes}
\aliasA{pamr.xl.get.offset}{pamr-internal}{pamr.xl.get.offset}
\aliasA{pamr.xl.get.sample.prior}{pamr-internal}{pamr.xl.get.sample.prior}
\aliasA{pamr.xl.get.soft.class.labels}{pamr-internal}{pamr.xl.get.soft.class.labels}
\aliasA{pamr.xl.get.threshold.range}{pamr-internal}{pamr.xl.get.threshold.range}
\aliasA{pamr.xl.get.uniform.prior}{pamr-internal}{pamr.xl.get.uniform.prior}
\aliasA{pamr.xl.is.a.subset}{pamr-internal}{pamr.xl.is.a.subset}
\aliasA{pamr.xl.listgenes.compute}{pamr-internal}{pamr.xl.listgenes.compute}
\aliasA{pamr.xl.plot.test.probs.compute}{pamr-internal}{pamr.xl.plot.test.probs.compute}
\aliasA{pamr.xl.plot.training.error.compute}{pamr-internal}{pamr.xl.plot.training.error.compute}
\aliasA{pamr.xl.plotcen.compute}{pamr-internal}{pamr.xl.plotcen.compute}
\aliasA{pamr.xl.plotcv.compute}{pamr-internal}{pamr.xl.plotcv.compute}
\aliasA{pamr.xl.plotcvprob.compute}{pamr-internal}{pamr.xl.plotcvprob.compute}
\aliasA{pamr.xl.plotsurvival}{pamr-internal}{pamr.xl.plotsurvival}
\methaliasA{pamr.xl.plotsurvival.strata}{pamr-internal}{pamr.xl.plotsurvival.strata}
\methaliasA{pamr.xl.plotsurvival.test}{pamr-internal}{pamr.xl.plotsurvival.test}
\aliasA{pamr.xl.predict.test.class}{pamr-internal}{pamr.xl.predict.test.class}
\methaliasA{pamr.xl.predict.test.class.only}{pamr-internal}{pamr.xl.predict.test.class.only}
\aliasA{pamr.xl.predict.test.probs}{pamr-internal}{pamr.xl.predict.test.probs}
\aliasA{pamr.xl.predict.test.surv.class}{pamr-internal}{pamr.xl.predict.test.surv.class}
\aliasA{pamr.xl.process.data}{pamr-internal}{pamr.xl.process.data}
\aliasA{pamr.xl.test.data.impute}{pamr-internal}{pamr.xl.test.data.impute}
\aliasA{pamr.xl.test.errors.compute}{pamr-internal}{pamr.xl.test.errors.compute}
\aliasA{pamr.xl.test.errors.surv.compute}{pamr-internal}{pamr.xl.test.errors.surv.compute}
\aliasA{pamr.xl.test.get.soft.classes}{pamr-internal}{pamr.xl.test.get.soft.classes}
\aliasA{pamr.xl.transform.class.labels}{pamr-internal}{pamr.xl.transform.class.labels}
\aliasA{pamr.xl.transform.data}{pamr-internal}{pamr.xl.transform.data}
\aliasA{pamr.xl.transform.test.data}{pamr-internal}{pamr.xl.transform.test.data}
\aliasA{print.nsc}{pamr-internal}{print.nsc}
\aliasA{print.nsccv}{pamr-internal}{print.nsccv}
\aliasA{print.pamrcved}{pamr-internal}{print.pamrcved}
\aliasA{print.pamrtrained}{pamr-internal}{print.pamrtrained}
\keyword{internal}{pamr-internal}
\begin{Description}\relax
Internal pamr functions
\end{Description}
\begin{Usage}
\begin{verbatim}
pamr.pairscore(x, pair.ind=NULL)
pamr.pvalue.survival(group, survival.time, censoring.status, ngroup.survival)
pamr.score.to.class1(x, scores, cutoff=2, n.class=2)
pamr.score.to.class2(x, scores, cutoff=2, n.pc=1, n.class=2)
pamr.knnimpute.old(data, k = 10) 
pamr.cube.root(x)
print.nsc(x, ...)
print.nsccv(x, ...)
print.pamrtrained(x, ...)
print.pamrcved(x, ...)
pamr.xl.error.trace() 
pamr.xl.get.threshold.range(fit) 
pamr.xl.get.soft.class.labels(fit, survival.times, censoring.status) 
pamr.xl.compute.offset(data, offset.percent=50, prior=prior)
pamr.xl.get.offset() 
pamr.xl.derive.adjusted.prior(prior, data) 
pamr.xl.get.default.training.parameters(data) 
pamr.xl.get.uniform.prior(data, nclasses=NULL) 
pamr.xl.get.sample.prior(data) 
pamr.xl.get.class.names() 
pamr.xl.get.class.labels() 
pamr.xl.get.number.of.classes() 
pamr.xl.process.data(use.old.version=FALSE) 
pamr.xl.compute.cv.confusion (fit, cv.results, threshold) 
pamr.xl.compute.confusion (fit, threshold) 
pamr.xl.is.a.subset(a, y) 
pamr.xl.listgenes.compute (fit, data, threshold, fitcv=NULL,  genenames = FALSE) 
pamr.xl.plot.test.probs.compute(fit, new.x, newx.classes, missing.class.label,threshold, sample.labels=NULL) 
pamr.xl.plot.training.error.compute(trained.object) 
pamr.xl.plotcen.compute(fit, data, threshold) 
pamr.xl.plotcv.compute(aa) 
pamr.xl.plotcvprob.compute(fit, data, threshold) 
pamr.xl.predict.test.class(fit, newx, threshold, test.class.labels) 
pamr.xl.predict.test.surv.class(fit, newx, threshold, survival.times, censoring.status) 
pamr.xl.predict.test.class.only(fit, newx, threshold) 
pamr.xl.predict.test.probs(fit, newx, threshold) 
pamr.xl.test.data.impute(x, k, use.old.version=FALSE) 
pamr.xl.test.errors.surv.compute(fit, newx, threshold=fit$threshold, survival.times, censoring.status) 
pamr.xl.test.errors.compute(fit, newx, newx.classes, threshold=fit$threshold, prior = fit$prior,  threshold.scale = fit$threshold.scale, ...) 
pamr.xl.transform.class.labels(x) 
pamr.xl.transform.data(data) 
pamr.xl.transform.test.data(test.x) 
pamr.xl.plotsurvival(fit, data, threshold) 
pamr.xl.plotsurvival.test(fit, newx, survival.time, censoring.status, threshold) 
pamr.xl.plotsurvival.strata(fit, data) 
pamr.xl.test.get.soft.classes(fit, survival.times, censoring.status)
pamr.xl.get.soft.class.labels(fit, survival.times, censoring.status) 

\end{verbatim}
\end{Usage}
\begin{Details}\relax
These are not to be called by the user.
\end{Details}
\begin{Author}\relax
Balasubramanian Narasimhan
and Rob Tibshirani
\end{Author}

