Man pages for seqCBS
Copy Number Profiling using Sequencing and CBS

BayesCptCIBayesian Point-wise Confidence Interval for Change-Point...
CombineCaseControlCCombine case and control reads
CombineReadsAcrossRunsCombine multiple read lists
getAutoGridSizeGet Automatic Grid Sizes
getCountsInWindowGet number of reads in fixed-width window
hppSimulateSimulate a homogeneous Poisson Process
JSSim_MetaMeta File for Simulated Datasets
JSSim_NormalSim1Simulated normal sample dataset 1
JSSim_NormalSim2Simulated normal sample dataset 2
JSSim_SpikeMatTrue Signal Spike for the Simulated Dataset
JSSim_TumorSim1Simulated Tumor sample dataset 1
JSSim_TumorSim2Simulated Tumor sample dataset 2
nhppRateEstimateEstimate the rate of non-homogeneous PP with data
nhppSimConstWindowAnalysisAnalyze the performance on simulation with constant signal...
nhppSimConstWindowGenSimulate a Non-Homogeneous PP with constant window spike
nhppSimulateSimulate a non-homogeneous Poisson Process
nhppSpikeSpike rates of NHPP
nhppSpikeConstWindowSpike NHPP rate with constant window width
readInputManage reading and merging of raw datasets. Main file input
readListInputFileRead meta file containing list of raw data files
readSeqWrapper for managing the reading of different raw data...
readSeqChiangRead data formatted as in Chiang (2009)
readSeqELANDPairedRead raw data formatted as in paired ELAND output
relCNCompCompute the Relative Copy Number
ScanBICCompute the modified BIC for change-point models
ScanCBSMain CBS Algorithm for Change-Point Detection
ScanCBSPlotMain Plotting of the scan statistic segmentation
ScanCBSSimPlotPlotting for CBS results of Simulated Data
ScanIterateGridMain Scan with Iterative Grid Search
ScanStatNewCompMain new window scan statistics computation
ScanStatRefineCompMain refining window scan statistics computation
SegSeqResProcessRead and Process result of SegSeq
seqCBS-packageScan Statistics CNV detection using sequencing data
seqCBS documentation built on May 2, 2019, 9:15 a.m.