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.

Install the latest version of this package by entering the following in R:
install.packages("seqCBS")
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

Functions

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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