cbind.SegList |
Combine SegList Objects |
chrominfo.Mb |
Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze |
combine.func |
Function 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 |
Retrieve the Dimensions of an RGList, MAList or SegList Object |
dim-method |
Retrieve the Dimensions of an RGList, MAList or SegList Object |
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 |
Retrieve the Dimension Names of an RGList, MAList or SegList Object |
dimnames-method |
Retrieve the Dimension Names 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 heterogeneous 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 |
Retrieve the Dimensions of an RGList, MAList or SegList Object |
length-method |
Retrieve the Dimensions of an RGList, MAList or SegList Object |
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 |
Function to merge states based on their state means |
MergeLevels.old |
Function to merge states based on their state means |
mergeStates |
Function to merge states based on their state means |
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 |
prop.na |
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 heterogeneous 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 |
runTilingArray |
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-method |
Large Data Object - class |
show-method |
Segmentation States - 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. |
zoomChromosome |
Interactive plot of a single chromsome |
zoomGenome |
Interactive plot of the whole genome |
[.SegList |
Segmentation States - class |