Man pages for seqCBS
Copy Number Profiling using Sequencing and CBS
| BayesCptCI | Bayesian Point-wise Confidence Interval for Change-Point... |
| 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 |
| 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 |
| 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 |
| 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 |
| seqCBS-package | Scan Statistics CNV detection using sequencing data |
