seqCBS: CN Profiling using Sequencing and CBS

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.

AuthorJeremy J. Shen, Nancy R. Zhang
Date of publication2012-10-29 08:59:40
MaintainerJeremy J. Shen <jeremyjshen@gmail.com>
LicenseGPL-2
Version1.2

View on CRAN

Man pages

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

Files in this package

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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