# pamr v1.55

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## Pam: prediction analysis for microarrays

Some functions for sample classification in microarrays

## Functions in pamr

Name | Description | |

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

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

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

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

pamr-internal | Internal pamr functions | |

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

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

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

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

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

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

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

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

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

khan | Khan microarray data | |

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

pamr.surv.to.class2 | A function to assign observations to categories, based on their survival times. | |

pamr.cv | A function to cross-validate the nearest shrunken centroid classifier | |

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

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

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

pamr.knnimpute | A function to impute missing expression data | |

pamr.plotstrata | A function to plot the survival curves in each Kaplan Meier stratum | |

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

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

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

pamr.confusion.survival | Compute confusin matrix from pamr survival fit | |

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## Details

License | GPL-2 |

Packaged | 2014-08-27 02:07:43 UTC; tibs |

Repository | CRAN |

Date/Publication | 2014-08-27 07:27:29 |

NeedsCompilation | yes |

depends | base (>= 2.10) , cluster , R (>= 2.10) , survival |

Contributors | Gil Chu, R. Tibshirani, Balasubramanian Narasimhan, T. Hastie |

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