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 |