seqCBS: CN Profiling using Sequencing and CBS
Version 1.2

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("seqCBS")

Getting started

Package overview

Popular man pages

JSSim_NormalSim1: Simulated normal sample dataset 1
nhppSpike: Spike rates of NHPP
readSeqELANDPaired: Read raw data formatted as in paired ELAND output
ScanBIC: Compute the modified BIC for change-point models
ScanIterateGrid: Main Scan with Iterative Grid Search
ScanStatNewComp: Main new window scan statistics computation
SegSeqResProcess: Read and Process result of SegSeq
See all...

All man pages Function index File listing

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

Functions

BayesCptCI Man page Source code
CombineCaseControlC Man page Source code
CombineReadsAcrossRuns Man page Source code
First.lib Source code
JSSim_Meta Man page
JSSim_NormalSim1 Man page
JSSim_NormalSim2 Man page
JSSim_SpikeMat Man page
JSSim_TumorSim1 Man page
JSSim_TumorSim2 Man page
ScanBIC Man page Source code
ScanCBS Man page Source code
ScanCBSPlot Man page Source code
ScanCBSSimPlot Man page Source code
ScanIterateGrid Man page Source code
ScanStatNewComp Man page Source code
ScanStatRefineComp Man page Source code
SegSeqResProcess Man page Source code
getAutoGridSize Man page Source code
getCountsInWindow Man page Source code
hppSimulate Man page Source code
nhppRateEstimate Man page Source code
nhppSimConstWindowAnalysis Man page Source code
nhppSimConstWindowGen Man page Source code
nhppSimulate Man page Source code
nhppSpike Man page Source code
nhppSpikeConstWindow Man page Source code
readInput Man page Source code
readListInputFile Man page Source code
readSeq Man page Source code
readSeqChiang Man page Source code
readSeqELANDPaired Man page Source code
relCNComp Man page Source code
seqCBS Man page
seqCBS-package Man page

Files

data
data/JSSim_SpikeMat.txt.gz
data/JSSim_NormalSim2.txt.xz
data/JSSim_NormalSim1.txt.xz
data/JSSim_TumorSim2.txt.xz
data/JSSim_TumorSim1.txt.xz
data/JSSim_Meta.txt.gz
src
src/seqCBS.c
NAMESPACE
man
man/nhppSimConstWindowAnalysis.Rd
man/readSeq.Rd
man/getAutoGridSize.Rd
man/JSSim_NormalSim2.Rd
man/ScanStatRefineComp.Rd
man/CombineReadsAcrossRuns.Rd
man/JSSim_TumorSim2.Rd
man/readSeqChiang.Rd
man/ScanIterateGrid.Rd
man/ScanBIC.Rd
man/readListInputFile.Rd
man/nhppSpikeConstWindow.Rd
man/getCountsInWindow.Rd
man/relCNComp.Rd
man/JSSim_Meta.Rd
man/nhppSimConstWindowGen.Rd
man/ScanStatNewComp.Rd
man/readInput.Rd
man/SegSeqResProcess.Rd
man/ScanCBSSimPlot.Rd
man/readSeqELANDPaired.Rd
man/JSSim_TumorSim1.Rd
man/ScanCBS.Rd
man/nhppSpike.Rd
man/BayesCptCI.Rd
man/JSSim_NormalSim1.Rd
man/CombineCaseControlC.Rd
man/hppSimulate.Rd
man/ScanCBSPlot.Rd
man/nhppRateEstimate.Rd
man/seqCBS-package.Rd
man/JSSim_SpikeMat.Rd
man/nhppSimulate.Rd
DESCRIPTION
MD5
R
R/ScanCBSPlot.R
R/nhppSimConstWindowGen.R
R/readListInputFile.R
R/CombineReadsAcrossRuns.R
R/readSeq.R
R/nhppSpikeConstWindow.R
R/getCountsInWindow.R
R/ScanBIC.R
R/nhppSimConstWindowAnalysis.R
R/SegSeqResProcess.R
R/hppSimulate.R
R/BayesCptCI.R
R/readSeqChiang.R
R/readSeqELANDPaired.R
R/ScanCBS.R
R/zz.R
R/ScanCBSSimPlot.R
R/nhppRateEstimate.R
R/nhppSpike.R
R/nhppSimulate.R
R/relCNComp.R
R/ScanIterateGrid.R
R/ScanStatNewComp.R
R/ScanStatRefineComp.R
R/readInput.R
R/getAutoGridSize.R
R/CombineCaseControlC.R
seqCBS documentation built on May 19, 2017, 10:53 a.m.

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