# Segmentation, normalisation and processing of aCGH data.

## Documentation for package `snapCGH' version 1.2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

cbind.SegList | Combine SegList Objects
chrominfo.Mb | Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze
combine.func | Funtion 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.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
findBreakPoints | Returns the start and end of segments.
fit.model | Fitting a heterogneous 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.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 | 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
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
nudSegmentation | Assigns each segment of each sample to either 'normal', 'up', 'down', 'amplified', or 'deleted'
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
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 heterogneous 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
runPicard | 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,LargeDataObject-method | Large Data Object - 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.
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
zoomChromosome | Interactive plot of a single chromsome
zoomGenome | Interactive plot of the whole genome
[.SegList | Subset SegList Objects