CombineCaseControlC | Combine case and control reads |
CombineReadsAcrossRuns | Combine multiple read lists |
getAutoGridSize | Get Automatic Grid Sizes |
getCountsInWindow | Get number of reads in fixed-width window |
hppSimulate | Simulate a homogeneous Poisson Process |
JSSim_Meta | Meta File for Simulated Datasets |
JSSim_NormalSim1 | Simulated normal sample dataset 1 |
JSSim_NormalSim2 | Simulated normal sample dataset 2 |
JSSim_SpikeMat | True Signal Spike for the Simulated Dataset |
JSSim_TumorSim1 | Simulated Tumor sample dataset 1 |
JSSim_TumorSim2 | Simulated Tumor sample dataset 2 |
nhppRateEstimate | Estimate the rate of non-homogeneous PP with data |
nhppSimConstWindow | Simulate a Non-Homogeneous PP with constant window spike |
nhppSimConstWindowAnalysis | Analyze the performance on simulation with constant signal... |
nhppSimConstWindowGen | Simulate a Non-Homogeneous PP with constant window spike |
nhppSimulate | Simulate a non-homogeneous Poisson Process |
nhppSpike | Spike rates of NHPP |
nhppSpikeConstSignal | Spike NHPP rate with constant signal strength |
nhppSpikeConstWindow | Spike NHPP rate with constant window width |
readInput | Manage reading and merging of raw datasets. Main file input |
readListInputFile | Read meta file containing list of raw data files |
readSeq | Wrapper for managing the reading of different raw data... |
readSeqChiang | Read data formatted as in Chiang (2009) |
readSeqELANDPaired | Read raw data formatted as in paired ELAND output |
readSeqJShen | Read my private data format |
readSeqMLove | Read Mike Love's private data format |
relCNComp | Compute the Relative Copy Number |
ScanBIC | Compute the modified BIC for change-point models |
ScanCBS | Main CBS Algorithm for Change-Point Detection |
ScanCBSPlot | Main Plotting of the scan statistic segmentation |
ScanCBSSimPlot | Plotting for CBS results of Simulated Data |
ScanIterateGrid | Main Scan with Iterative Grid Search |
ScanStatNewComp | Main new window scan statistics computation |
ScanStatRefineComp | Main refining window scan statistics computation |
SegSeqResProcess | Read and Process result of SegSeq |
SeqCNVCBS-package | Scan Statistics CNV detection using sequencing data |
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