cn.FARMS - factor analysis for copy number estimation

callSummarize | Defines which variables should be written back when calling a... |

cn.farms | cn.farms |

cnLibrary | This function was taken from snowfall and edited due to some... |

combineData | Combine two ExpressionSet objects |

createAnnotation | Creation of annotation files |

createMatrix | Creates the needed matrix |

distributionDistance | Computes the distribution distance |

dnaCopySf | Runs DNAcopy in parallel mode |

doCnFarmsSingle | Does the whole cn.farms process in one call |

flcSnp6Std | Does a fragment length correction on intensities |

flcStd | Does a fragment length correction on intensities |

fragLengCorr | Does a fragment length correction |

getFragmentSet | Finds SNPs which belong to one fragment |

getSingleProbeSetSize | Combines data for probeset summarization |

mlSummarization | Method for computation of the multi-loci summarization |

normAdd | Extracts info from the package name |

normalizeAverage | Scales the range of the non-polymorphic data to the range of... |

normalizeCels | Wrapper for the normalization functions |

normalizeNone | Runs the SOR normalization on microarray data |

normalizeNpData | Processes the non-polymorphic data |

normalizeQuantiles | Normalization Quantiles |

normalizeSequenceEffect | Correction for probe sequence effects |

normalizeSor | Runs the SOR normalization on microarray data |

plotDendrogram | Plots a dendrogram |

plotDensity | Function to create a density plot |

plotEvalIc | Creates a plot with known regions and a numeric vector |

plotRegions | Plots given regions by segments |

plotSmoothScatter | Creates a smooth scatter plot |

plotViolines | Create a violine plot |

slSummarization | Method for computation of the single-locus summarization |

sparseFarmsC | Normalizes the data with SOR |

summarizeFarmsExact | Summarization Laplacian approach with exact computation |

summarizeFarmsExact2 | Summarization Laplacian approach with exact computation |

summarizeFarmsExact3 | Summarization Laplacian approach with exact computation |

summarizeFarmsGaussian | Summarization Gaussian approach |

summarizeFarmsMethods | Lists methods for possible FARMS summarization |

summarizeFarmsStatistics | Mean or median instead of the FARMS model |

summarizeFarmsVariational | Summarization variational Laplacian approach |

summarizeWindowBps | Combines neighbouring locations to windows |

summarizeWindowMethods | Lists methods for possible window methods |

summarizeWindowStd | Combines neighbouring locations to windows |

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