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.

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

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