This is a method for DNA Copy Number Profiling using Next-Generation Sequencing. It has new model and test statistics based on non-homogeneous Poisson Processes with change point models. It uses an adaptation of Circular Binary Segmentation. Also included are methods for point-wise Bayesian Confidence Interval and model selection method for the change-point model. A case and a control sample reads (normal and tumor) are required.

Author | Jeremy J. Shen, Nancy R. Zhang |

Date of publication | 2012-10-29 08:59:40 |

Maintainer | Jeremy J. Shen <jeremyjshen@gmail.com> |

License | GPL-2 |

Version | 1.2 |

**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

seqCBS

seqCBS/data

seqCBS/data/JSSim_SpikeMat.txt.gz

seqCBS/data/JSSim_NormalSim2.txt.xz

seqCBS/data/JSSim_NormalSim1.txt.xz

seqCBS/data/JSSim_TumorSim2.txt.xz

seqCBS/data/JSSim_TumorSim1.txt.xz

seqCBS/data/JSSim_Meta.txt.gz

seqCBS/src

seqCBS/src/seqCBS.c

seqCBS/NAMESPACE

seqCBS/man

seqCBS/man/nhppSimConstWindowAnalysis.Rd
seqCBS/man/readSeq.Rd
seqCBS/man/getAutoGridSize.Rd
seqCBS/man/JSSim_NormalSim2.Rd
seqCBS/man/ScanStatRefineComp.Rd
seqCBS/man/CombineReadsAcrossRuns.Rd
seqCBS/man/JSSim_TumorSim2.Rd
seqCBS/man/readSeqChiang.Rd
seqCBS/man/ScanIterateGrid.Rd
seqCBS/man/ScanBIC.Rd
seqCBS/man/readListInputFile.Rd
seqCBS/man/nhppSpikeConstWindow.Rd
seqCBS/man/getCountsInWindow.Rd
seqCBS/man/relCNComp.Rd
seqCBS/man/JSSim_Meta.Rd
seqCBS/man/nhppSimConstWindowGen.Rd
seqCBS/man/ScanStatNewComp.Rd
seqCBS/man/readInput.Rd
seqCBS/man/SegSeqResProcess.Rd
seqCBS/man/ScanCBSSimPlot.Rd
seqCBS/man/readSeqELANDPaired.Rd
seqCBS/man/JSSim_TumorSim1.Rd
seqCBS/man/ScanCBS.Rd
seqCBS/man/nhppSpike.Rd
seqCBS/man/BayesCptCI.Rd
seqCBS/man/JSSim_NormalSim1.Rd
seqCBS/man/CombineCaseControlC.Rd
seqCBS/man/hppSimulate.Rd
seqCBS/man/ScanCBSPlot.Rd
seqCBS/man/nhppRateEstimate.Rd
seqCBS/man/seqCBS-package.Rd
seqCBS/man/JSSim_SpikeMat.Rd
seqCBS/man/nhppSimulate.Rd
seqCBS/DESCRIPTION

seqCBS/MD5

seqCBS/R

seqCBS/R/ScanCBSPlot.R
seqCBS/R/nhppSimConstWindowGen.R
seqCBS/R/readListInputFile.R
seqCBS/R/CombineReadsAcrossRuns.R
seqCBS/R/readSeq.R
seqCBS/R/nhppSpikeConstWindow.R
seqCBS/R/getCountsInWindow.R
seqCBS/R/ScanBIC.R
seqCBS/R/nhppSimConstWindowAnalysis.R
seqCBS/R/SegSeqResProcess.R
seqCBS/R/hppSimulate.R
seqCBS/R/BayesCptCI.R
seqCBS/R/readSeqChiang.R
seqCBS/R/readSeqELANDPaired.R
seqCBS/R/ScanCBS.R
seqCBS/R/zz.R
seqCBS/R/ScanCBSSimPlot.R
seqCBS/R/nhppRateEstimate.R
seqCBS/R/nhppSpike.R
seqCBS/R/nhppSimulate.R
seqCBS/R/relCNComp.R
seqCBS/R/ScanIterateGrid.R
seqCBS/R/ScanStatNewComp.R
seqCBS/R/ScanStatRefineComp.R
seqCBS/R/readInput.R
seqCBS/R/getAutoGridSize.R
seqCBS/R/CombineCaseControlC.R
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