Entry: IDProbes
Aliases: IDProbes
Keywords: hplot
Description: Interactive version of genomePlot
URL: ../../../library/snapCGH/html/IDProbes.html

Entry: LargeDataObject-class
Aliases: LargeDataObject-class show,LargeDataObject-method
Keywords: classes data
Description: Large Data Object - class
URL: ../../../library/snapCGH/html/LargeDataObject.html

Entry: SegList-class
Aliases: SegList-class print.SegList show,SegList-method [.SegList
Keywords: classes data
Description: Segmentation States - class
URL: ../../../library/snapCGH/html/SegList.html

Entry: Viterbi.five
Aliases: Viterbi.five
Keywords: misc
Description: A scaled Viterbi algorithm for allocating clones to one of five underlying states.
URL: ../../../library/snapCGH/html/Viterbi.five.html

Entry: Viterbi.four
Aliases: Viterbi.four
Keywords: misc
Description: A scaled Viterbi algorithm for allocating clones to one of four underlying states.
URL: ../../../library/snapCGH/html/Viterbi.four.html

Entry: Viterbi.three
Aliases: Viterbi.three
Keywords: misc
Description: A scaled Viterbi algorithm for allocating clones to one of two underlying states.
URL: ../../../library/snapCGH/html/Viterbi.three.html

Entry: Viterbi.two
Aliases: Viterbi.two
Keywords: misc
Description: A scaled Viterbi algorithm for allocating clones to one of two underlying states.
URL: ../../../library/snapCGH/html/Viterbi.two.html

Entry: cbind
Aliases: cbind.SegList rbind.SegList
Keywords: manip
Description: Combine SegList Objects
URL: ../../../library/snapCGH/html/cbind.html

Entry: chrominfo.Mb
Aliases: chrominfo.Mb
Keywords: datasets
Description: Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze
URL: ../../../library/snapCGH/html/chrominfo.Mb.html

Entry: compareSegmentations
Aliases: compareSegmentations compareBreakPoints
Keywords: manip
Description: Function for comparing segmentation methods to a known truth
URL: ../../../library/snapCGH/html/compareSegmentations.html

Entry: convert.output
Aliases: convert.output
Keywords: datasets
Description: Converts the output from the simulation to a format which can be used by segmentation schemes available within R
URL: ../../../library/snapCGH/html/convert.output.html

Entry: dim
Aliases: dim length dim.RGList dim.MAList dim.SegList dim,SegList-method length.RGList length.MAList length.SegList length,SegList-method
Keywords: array
Description: Retrieve the Dimensions of an RGList, MAList or SegList Object
URL: ../../../library/snapCGH/html/dim.html

Entry: dimnames
Aliases: dimnames dimnames,SegList-method dimnames.SegList
Keywords: array
Description: Retrieve the Dimension Names of an RGList, MAList or SegList Object
URL: ../../../library/snapCGH/html/dimnames.html

Entry: filterClones
Aliases: filterClones
Keywords: methods
Description: Filter clones from sample
URL: ../../../library/snapCGH/html/filter.html

Entry: find.param.five
Aliases: find.param.five
Keywords: misc
Description: Yields the output in a model with five underlying states
URL: ../../../library/snapCGH/html/find.param.five.html

Entry: find.param.four
Aliases: find.param.four
Keywords: misc
Description: Yields output when there are 4 underlying states
URL: ../../../library/snapCGH/html/find.param.four.html

Entry: find.param.one
Aliases: find.param.one
Keywords: misc
Description: Yields output when there is 1 underlying states
URL: ../../../library/snapCGH/html/find.param.one.html

Entry: find.param.three
Aliases: find.param.three
Keywords: misc
Description: Yields output when there are 3 underlying states
URL: ../../../library/snapCGH/html/find.param.three.html

Entry: find.param.two
Aliases: find.param.two
Keywords: misc
Description: Yields output when there are 2 underlying states
URL: ../../../library/snapCGH/html/find.param.two.html

Entry: findBreakPoints
Aliases: findBreakPoints
Keywords: methods
Description: Returns the start and end of segments.
URL: ../../../library/snapCGH/html/findBreakPoints.html

Entry: fit.model
Aliases: fit.model run.nelder
Keywords: models
Description: Fitting a heterogneous HMM to the log2 ratios on a particular chromosome.
URL: ../../../library/snapCGH/html/fit.model.html

Entry: genomePlot
Aliases: genomePlot sample.names
Keywords: hplot
Description: Plots the genome
URL: ../../../library/snapCGH/html/genomePlot.html

Entry: heatmapGenome
Aliases: heatmapGenome plotvalChrom.func plotValGenome plotValChrom plotChrom maPalette floor.func
Keywords: hplot cluster
Description: clustering and heatmap
URL: ../../../library/snapCGH/html/heatmapGenome.html

Entry: imputeMissingValues
Aliases: imputeMissingValues
Keywords: models
Description: Imputing log2 ratios
URL: ../../../library/snapCGH/html/imputeMissingValues.html

Entry: log2ratios
Aliases: log2ratios
Keywords: datasets
Description: Extracting log2 ratios
URL: ../../../library/snapCGH/html/log2ratios.html

Entry: mergeStates
Aliases: mergeStates MergeLevels.new MergeLevels.old combine.func
Keywords: models
Description: Funtion to merge states based on their state means
URL: ../../../library/snapCGH/html/mergeStates.html

Entry: non.zero.length.distr.non.tiled
Aliases: non.zero.length.distr.non.tiled
Keywords: datasets
Description: Empirical distribution of segment lengths in non-tiled regions with copy number gains or losses
URL: ../../../library/snapCGH/html/non.zero.length.distr.non.tiled.html

Entry: non.zero.length.distr.tiled
Aliases: non.zero.length.distr.tiled
Keywords: datasets
Description: Empirical distribution of segment lengths in tiled regions with copy number gains or losses
URL: ../../../library/snapCGH/html/non.zero.length.distr.tiled.html

Entry: plotSegmentedGenome
Aliases: plotSegmentedGenome
Keywords: hplot
Description: Plots the genome
URL: ../../../library/snapCGH/html/plotSegmentedGenome.html

Entry: processCGH
Aliases: processCGH prop.na
Keywords: file
Description: Process data in an MAList
URL: ../../../library/snapCGH/html/processCGH.html

Entry: read.clonesinfo
Aliases: read.clonesinfo
Keywords: methods
Description: Reading chromsome and positional information about each clone.
URL: ../../../library/snapCGH/html/read.clonesinfo.html

Entry: readPositionalInfo
Aliases: readPositionalInfo
Keywords: manip
Description: readPositionalInfo
URL: ../../../library/snapCGH/html/readPositionalInfo.html

Entry: removeByWeights
Aliases: removeByWeights
Keywords: methods
Description: Remove clones based on a weights matrix
URL: ../../../library/snapCGH/html/removeByWeights.html

Entry: runBioHMM
Aliases: runBioHMM
Keywords: models
Description: This function implements the BioHMM
URL: ../../../library/snapCGH/html/runBioHMM.html

Entry: runDNAcopy
Aliases: runDNAcopy
Keywords: methods
Description: Results of segmenting an MAList data object using the DNAcopy library
URL: ../../../library/snapCGH/html/runDNAcopy.html

Entry: runGLAD
Aliases: runGLAD
Keywords: methods
Description: Results of segmenting an aCGHList data object using the GLAD library
URL: ../../../library/snapCGH/html/runGLAD.html

Entry: runHomHMM
Aliases: runHomHMM states.hmm.func
Keywords: models
Description: A function to fit unsupervised Hidden Markov model
URL: ../../../library/snapCGH/html/runHMM.html

Entry: runTilingArray
Aliases: runTilingArray
Keywords: methods
Description: Results of segmenting an MAList data object using the Picard et al algorithm found in the tilingArray library
URL: ../../../library/snapCGH/html/runTilingArray.html

Entry: simulateData
Aliases: simulateData generate.data
Keywords: datasets
Description: A function for simulating aCGH data and the corresponding clone layout
URL: ../../../library/snapCGH/html/sim.structure.html

Entry: zero.length.distr.non.tiled
Aliases: zero.length.distr.non.tiled
Keywords: datasets
Description: Empirical distribution of segment lengths in non-tiled regions with no copy number gains or losses
URL: ../../../library/snapCGH/html/zero.length.distr.non.tiled.html

Entry: zero.length.distr.tiled
Aliases: zero.length.distr.tiled
Keywords: datasets
Description: Empirical distribution of segment lengths in tiled regions with no copy number gains or losses
URL: ../../../library/snapCGH/html/zero.length.distr.tiled.html

Entry: zoomChromosome
Aliases: zoomChromosome
Keywords: hplot
Description: Interactive plot of a single chromsome
URL: ../../../library/snapCGH/html/zoomChromosome.html

Entry: zoomGenome
Aliases: zoomGenome
Keywords: hplot
Description: Interactive plot of the whole genome
URL: ../../../library/snapCGH/html/zoomGenome.html
