Segmentation, normalisation and processing of aCGH data.


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Documentation for package `snapCGH' version 1.0.0

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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