Man pages for snapCGH
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 |
| 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... |
| zoomChromosome | Interactive plot of a single chromsome |
| zoomGenome | Interactive plot of the whole genome |
