Segmentation, normalisation and processing of aCGH data.

cbind | Combine SegList Objects |

chrominfo.Mb | Basic Chromosomal Information for UCSC Human Genome Assembly... |

compareSegmentations | Function for comparing segmentation methods to a known truth |

convert.output | Converts the output from the simulation to a format which can... |

dim | Retrieve the Dimensions of an RGList, MAList or SegList... |

dimnames | Retrieve the Dimension Names of an RGList, MAList or SegList... |

filter | Filter clones from sample |

findBreakPoints | Returns the start and end of segments. |

find.param.five | Yields the output in a model with five underlying states |

find.param.four | Yields output when there are 4 underlying states |

find.param.one | Yields output when there is 1 underlying states |

find.param.three | Yields output when there are 3 underlying states |

find.param.two | Yields output when there are 2 underlying states |

fit.model | Fitting a heterogeneous HMM to the log2 ratios on a... |

genomePlot | Plots the genome |

heatmapGenome | clustering and heatmap |

IDProbes | Interactive version of genomePlot |

imputeMissingValues | Imputing log2 ratios |

LargeDataObject | Large Data Object - class |

log2ratios | Extracting log2 ratios |

mergeStates | Function to merge states based on their state means |

non.zero.length.distr.non.tiled | Empirical distribution of segment lengths in non-tiled... |

non.zero.length.distr.tiled | Empirical distribution of segment lengths in tiled regions... |

plotSegmentedGenome | Plots the genome |

processCGH | Process data in an MAList |

read.clonesinfo | Reading chromsome and positional information about each... |

readPositionalInfo | readPositionalInfo |

removeByWeights | Remove clones based on a weights matrix |

runBioHMM | This function implements the BioHMM |

runDNAcopy | Results of segmenting an MAList data object using the DNAcopy... |

runGLAD | Results of segmenting an aCGHList data object using the GLAD... |

runHMM | A function to fit unsupervised Hidden Markov model |

runTilingArray | Results of segmenting an MAList data object using the Picard... |

SegList | Segmentation States - class |

sim.structure | A function for simulating aCGH data and the corresponding... |

Viterbi.five | A scaled Viterbi algorithm for allocating clones to one of... |

Viterbi.four | A scaled Viterbi algorithm for allocating clones to one of... |

Viterbi.three | A scaled Viterbi algorithm for allocating clones to one of... |

Viterbi.two | A scaled Viterbi algorithm for allocating clones to one of... |

zero.length.distr.non.tiled | Empirical distribution of segment lengths in non-tiled... |

zero.length.distr.tiled | Empirical distribution of segment lengths in tiled regions... |

zoomChromosome | Interactive plot of a single chromsome |

zoomGenome | Interactive plot of the whole genome |

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