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| cbind.SegList | Combine SegList Objects |
| chrominfo.Mb | Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze |
| combine.func | Function to merge states based on their state means |
| compareBreakPoints | Function for comparing segmentation methods to a known truth |
| compareSegmentations | Function for comparing segmentation methods to a known truth |
| convert.output | Converts the output from the simulation to a format which can be used by segmentation schemes available within R |
| dim | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| dim-method | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| dim.MAList | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| dim.RGList | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| dim.SegList | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| dimnames | Retrieve the Dimension Names of an RGList, MAList or SegList Object |
| dimnames-method | Retrieve the Dimension Names of an RGList, MAList or SegList Object |
| dimnames.SegList | Retrieve the Dimension Names of an RGList, MAList or SegList Object |
| filterClones | Filter clones from sample |
| 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 |
| findBreakPoints | Returns the start and end of segments. |
| fit.model | Fitting a heterogeneous HMM to the log2 ratios on a particular chromosome. |
| floor.func | clustering and heatmap |
| generate.data | A function for simulating aCGH data and the corresponding clone layout |
| genomePlot | Plots the genome |
| heatmapGenome | clustering and heatmap |
| IDProbes | Interactive version of genomePlot |
| imputeMissingValues | Imputing log2 ratios |
| LargeDataObject-class | Large Data Object - class |
| length | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| length-method | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| length.MAList | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| length.RGList | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| length.SegList | Retrieve the Dimensions of an RGList, MAList or SegList Object |
| log2ratios | Extracting log2 ratios |
| maPalette | clustering and heatmap |
| MergeLevels.new | Function to merge states based on their state means |
| MergeLevels.old | Function to merge states based on their state means |
| mergeStates | Function to merge states based on their state means |
| plotChrom | clustering and heatmap |
| plotSegmentedGenome | Plots the genome |
| plotValChrom | clustering and heatmap |
| plotvalChrom.func | clustering and heatmap |
| plotValGenome | clustering and heatmap |
| print.SegList | Segmentation States - class |
| processCGH | Process data in an MAList |
| prop.na | Process data in an MAList |
| rbind.SegList | Combine SegList Objects |
| read.clonesinfo | Reading chromsome and positional information about each clone. |
| readPositionalInfo | readPositionalInfo |
| removeByWeights | Remove clones based on a weights matrix |
| run.nelder | Fitting a heterogeneous HMM to the log2 ratios on a particular chromosome. |
| runBioHMM | This function implements the BioHMM |
| runDNAcopy | Results of segmenting an MAList data object using the DNAcopy library |
| runGLAD | Results of segmenting an aCGHList data object using the GLAD library |
| runHomHMM | A function to fit unsupervised Hidden Markov model |
| runTilingArray | Results of segmenting an MAList data object using the Picard et al algorithm found in the tilingArray library |
| sample.names | Plots the genome |
| SegList-class | Segmentation States - class |
| show-method | Large Data Object - class |
| show-method | Segmentation States - class |
| simulateData | A function for simulating aCGH data and the corresponding clone layout |
| states.hmm.func | A function to fit unsupervised Hidden Markov model |
| Viterbi.five | A scaled Viterbi algorithm for allocating clones to one of five underlying states. |
| Viterbi.four | A scaled Viterbi algorithm for allocating clones to one of four underlying states. |
| Viterbi.three | A scaled Viterbi algorithm for allocating clones to one of two underlying states. |
| Viterbi.two | A scaled Viterbi algorithm for allocating clones to one of two underlying states. |
| zoomChromosome | Interactive plot of a single chromsome |
| zoomGenome | Interactive plot of the whole genome |
| [.SegList | Segmentation States - class |