Entry: GEList-class
Aliases: GEList-class
Keywords: classes data
Description: Genomic Events - class
URL: ../../../library/snapCGH/html/GEList.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
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
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: computeSD
Aliases: computeSD
Keywords: models
Description: Function to estimate experimental variability of a sample
URL: ../../../library/snapCGH/html/computeSD.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.RGList dim.MAList dim.SegList length.RGList length.MAList length.SegList
Keywords: array
Description: Retrieve the Dimensions of an RGList, MAList or SegList Object
URL: ../../../library/snapCGH/html/dim.html

Entry: dimnames
Aliases: 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: findAberrations
Aliases: findAberrations
Keywords: models
Description: Function to determines focal aberrations
URL: ../../../library/snapCGH/html/findAberrations.html

Entry: findAmplifications
Aliases: findAmplifications
Keywords: models
Description: Function to determine high level amplifications
URL: ../../../library/snapCGH/html/findAmplifications.html

Entry: findBreakPoints
Aliases: findBreakPoints
Keywords: models
Description: ~~function to do ... ~~
URL: ../../../library/snapCGH/html/findBreakPoints.html

Entry: findGenomicEvents
Aliases: findGenomicEvents
Keywords: models
Description: Finds the genomic events associated with each of the array CGH samples
URL: ../../../library/snapCGH/html/findGenomicEvents.html

Entry: findOutliers
Aliases: findOutliers
Keywords: models
Description: Function to identify outlier clones
URL: ../../../library/snapCGH/html/findOutliers.html

Entry: findTranslocations
Aliases: findTranslocations
Keywords: models
Description: Funtion identifying the transitions
URL: ../../../library/snapCGH/html/findTranslocations.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: fitBioHMM
Aliases: fitBioHMM
Keywords: models
Description: This function implements the BioHMM
URL: ../../../library/snapCGH/html/fitBioHMM.html

Entry: runHomHMM
Aliases: runHomHMM mu1.func states.hmm.func
Keywords: models
Description: A function to fit unsupervised Hidden Markov model
URL: ../../../library/snapCGH/html/fitHMM.html

Entry: fractionAltered
Aliases: fractionAltered
Keywords: htest
Description: Function to compute fraction of genome altered for each sample
URL: ../../../library/snapCGH/html/fractionAltered.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/impute.lowess.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: mod.chrominfo
Aliases: mod.chrominfo
Keywords: datasets
Description: Chromosomal information
URL: ../../../library/snapCGH/html/mod.chrominfo.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: plotGainLoss
Aliases: plotGainLoss changeProp.func changeProp.overall.func table.bac.func lengthGain.na propGain.na lengthLoss.na propLoss.na prop.na create.resT
Keywords: htest hplot
Description: frequency plots and significance analysis
URL: ../../../library/snapCGH/html/plotGainLoss.html

Entry: plotSegmentationStates
Aliases: plotSegmentationStates
Keywords: hplot
Description: Plotting the estimated hmm states and log2 ratios for each sample.
URL: ../../../library/snapCGH/html/plotSegmentationStates.html

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

Entry: plotSegmentationSummary
Aliases: plotSegmentationSummary prop.num.func
Keywords: hplot
Description: plotSegmentationSummary
URL: ../../../library/snapCGH/html/plotSummaryProfile.html

Entry: processCGH
Aliases: processCGH
Keywords: file
Description: Process data in aCGH object
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: removeByWeights
Aliases: removeByWeights
Keywords: methods
Description: Remove clones based on a weights matrix
URL: ../../../library/snapCGH/html/removeByWeights.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: sim.structure
Aliases: sim.structure
Keywords: datasets
Description: A function for simulating aCGH data and the corresponding clone layout
URL: ../../../library/snapCGH/html/sim.structure.html

Entry: subsetting
Aliases: [.SegList
Keywords: manip
Description: Subset SegList Objects
URL: ../../../library/snapCGH/html/subsetting.html

Entry: summarizeClones
Aliases: summarizeClones
Keywords: models
Description: Extracting summary information for all clones
URL: ../../../library/snapCGH/html/summarize.clones.html

Entry: threshold
Aliases: threshold
Keywords: htest
Description: Function to indicate gain or loss for each clone for each sample
URL: ../../../library/snapCGH/html/threshold.func.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
