BayesCptCI              Bayesian Point-wise Confidence Interval for
                        Change-Point Model
CombineCaseControlC     Combine case and control reads
CombineReadsAcrossRuns
                        Combine multiple read lists
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
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
getAutoGridSize         Get Automatic Grid Sizes
getCountsInWindow       Get number of reads in fixed-width window
hppSimulate             Simulate a homogeneous Poisson Process
nhppRateEstimate        Estimate the rate of non-homogeneous PP with
                        data
nhppSimConstWindowAnalysis
                        Analyze the performance on simulation with
                        constant signal length in each set
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 formats
readSeqChiang           Read data formatted as in Chiang (2009)
readSeqELANDPaired      Read raw data formatted as in paired ELAND
                        output
relCNComp               Compute the Relative Copy Number
seqCBS-package          Scan Statistics CNV detection using sequencing
                        data
