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| cbind.SegList | Combine SegList Objects |
| changeProp.func | frequency plots and significance analysis |
| changeProp.overall.func | frequency plots and significance analysis |
| chrominfo.Mb | Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze |
| combine.func | Funtion to merge states based on their state means |
| computeSD | Function to estimate experimental variability of a sample |
| convert.output | Converts the output from the simulation to a format which can be used by segmentation schemes available within R |
| create.resT | frequency plots and significance analysis |
| 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.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 |
| findAberrations | Function to determines focal aberrations |
| findAmplifications | Function to determine high level amplifications |
| findBreakPoints | ~~function to do ... ~~ |
| findGenomicEvents | Finds the genomic events associated with each of the array CGH samples |
| findOutliers | Function to identify outlier clones |
| findTranslocations | Funtion identifying the transitions |
| fit.model | Fitting a heterogneous HMM to the log2 ratios on a particular chromosome. |
| fitBioHMM | This function implements the BioHMM |
| floor.func | clustering and heatmap |
| fractionAltered | Function to compute fraction of genome altered for each sample |
| GEList-class | Genomic Events - class |
| genomePlot | Plots the genome |
| heatmapGenome | clustering and heatmap |
| imputeMissingValues | Imputing log2 ratios |
| LargeDataObject-class | Large Data Object - class |
| 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 |
| lengthGain.na | frequency plots and significance analysis |
| lengthLoss.na | frequency plots and significance analysis |
| log2ratios | Extracting log2 ratios |
| maPalette | clustering and heatmap |
| MergeLevels.new | Funtion to merge states based on their state means |
| MergeLevels.old | Funtion to merge states based on their state means |
| mergeStates | Funtion to merge states based on their state means |
| mod.chrominfo | Chromosomal information |
| mu1.func | A function to fit unsupervised Hidden Markov model |
| non.zero.length.distr.non.tiled | Empirical distribution of segment lengths in non-tiled regions with copy number gains or losses |
| non.zero.length.distr.tiled | Empirical distribution of segment lengths in tiled regions with copy number gains or losses |
| plotChrom | clustering and heatmap |
| plotGainLoss | frequency plots and significance analysis |
| plotSegmentationStates | Plotting the estimated hmm states and log2 ratios for each sample. |
| plotSegmentationSummary | plotSegmentationSummary |
| 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 aCGH object |
| prop.na | frequency plots and significance analysis |
| prop.num.func | plotSegmentationSummary |
| propGain.na | frequency plots and significance analysis |
| propLoss.na | frequency plots and significance analysis |
| read.clonesinfo | Reading chromsome and positional information about each clone. |
| removeByWeights | Remove clones based on a weights matrix |
| run.nelder | Fitting a heterogneous HMM to the log2 ratios on a particular chromosome. |
| 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 |
| sample.names | Plots the genome |
| SegList-class | Segmentation States - class |
| show,LargeDataObject-method | Large Data Object - class |
| sim.structure | A function for simulating aCGH data and the corresponding clone layout |
| states.hmm.func | A function to fit unsupervised Hidden Markov model |
| summarizeClones | Extracting summary information for all clones |
| table.bac.func | frequency plots and significance analysis |
| threshold | Function to indicate gain or loss for each clone for each sample |
| 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. |
| zero.length.distr.non.tiled | Empirical distribution of segment lengths in non-tiled regions with no copy number gains or losses |
| zero.length.distr.tiled | Empirical distribution of segment lengths in tiled regions with no copy number gains or losses |
| [.SegList | Subset SegList Objects |