SeqCNVCBS: Scan Statistics for CNV Detection with CBS

This package is for the use of detecting Copy Number Variation (CNV) using sequencing data. Matched-samples of control and case (normal and tumor) are required. The algorithm uses a scan statistics to detect windows of rate differences in two non-homogeneous Poisson Processes.

AuthorJeremy J. Shen, Nancy R. Zhang
Date of publicationNone
MaintainerJeremy J. Shen <jqshen@stanford.edu>
LicenseGPL-2
Version1.0

View on R-Forge

Man pages

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

nhppSimConstWindow: Simulate a Non-Homogeneous PP with constant window spike

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

nhppSpikeConstSignal: Spike NHPP rate with constant signal strength

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

readSeqJShen: Read my private data format

readSeqMLove: Read Mike Love's private data format

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

SeqCNVCBS-package: Scan Statistics CNV detection using sequencing data

Files in this package

SeqCNVCBS
SeqCNVCBS/NAMESPACE
SeqCNVCBS/data
SeqCNVCBS/data/JSSim_TumorSim2.txt.gz
SeqCNVCBS/data/JSSim_TumorSim1.txt.gz
SeqCNVCBS/data/JSSim_SpikeMat.txt.gz
SeqCNVCBS/data/JSSim_NormalSim2.txt.gz
SeqCNVCBS/data/JSSim_NormalSim1.txt.gz
SeqCNVCBS/data/JSSim_Meta.txt.gz
SeqCNVCBS/R
SeqCNVCBS/R/zz.R SeqCNVCBS/R/readSeqMLove.R SeqCNVCBS/R/readInput.R SeqCNVCBS/R/CombineReadsAcrossRuns.R SeqCNVCBS/R/nhppSimConstWindowGen.R SeqCNVCBS/R/ScanStatRefineComp.R SeqCNVCBS/R/readSeq.R SeqCNVCBS/R/ScanCBSSimPlot.R SeqCNVCBS/R/nhppSimConstWindowAnalysis.R SeqCNVCBS/R/SegSeqResProcess.R SeqCNVCBS/R/readSeqJShen.R SeqCNVCBS/R/ScanBIC.R SeqCNVCBS/R/nhppRateEstimate.R SeqCNVCBS/R/getCountsInWindow.R SeqCNVCBS/R/ScanCBS.R SeqCNVCBS/R/nhppSpikeConstSignal.R SeqCNVCBS/R/hppSimulate.R SeqCNVCBS/R/CombineCaseControlC.R SeqCNVCBS/R/readListInputFile.R SeqCNVCBS/R/getAutoGridSize.R SeqCNVCBS/R/nhppSimConstWindow.R SeqCNVCBS/R/ScanIterateGrid.R SeqCNVCBS/R/ScanStatNewComp.R SeqCNVCBS/R/readSeqELANDPaired.R SeqCNVCBS/R/nhppSpikeConstWindow.R SeqCNVCBS/R/readSeqChiang.R SeqCNVCBS/R/ScanCBSPlot.R SeqCNVCBS/R/nhppSimulate.R SeqCNVCBS/R/relCNComp.R SeqCNVCBS/R/nhppSpike.R
SeqCNVCBS/DESCRIPTION
SeqCNVCBS/man
SeqCNVCBS/man/ScanCBS.Rd SeqCNVCBS/man/nhppSimulate.Rd SeqCNVCBS/man/readSeqChiang.Rd SeqCNVCBS/man/JSSim_TumorSim2.Rd SeqCNVCBS/man/readSeq.Rd SeqCNVCBS/man/ScanBIC.Rd SeqCNVCBS/man/SeqCNVCBS-package.Rd SeqCNVCBS/man/nhppRateEstimate.Rd SeqCNVCBS/man/nhppSpikeConstSignal.Rd SeqCNVCBS/man/nhppSimConstWindowAnalysis.Rd SeqCNVCBS/man/JSSim_NormalSim2.Rd SeqCNVCBS/man/CombineCaseControlC.Rd SeqCNVCBS/man/nhppSpike.Rd SeqCNVCBS/man/readSeqMLove.Rd SeqCNVCBS/man/CombineReadsAcrossRuns.Rd SeqCNVCBS/man/hppSimulate.Rd SeqCNVCBS/man/JSSim_Meta.Rd SeqCNVCBS/man/readSeqELANDPaired.Rd SeqCNVCBS/man/getCountsInWindow.Rd SeqCNVCBS/man/relCNComp.Rd SeqCNVCBS/man/ScanStatNewComp.Rd SeqCNVCBS/man/getAutoGridSize.Rd SeqCNVCBS/man/readListInputFile.Rd SeqCNVCBS/man/SegSeqResProcess.Rd SeqCNVCBS/man/nhppSpikeConstWindow.Rd SeqCNVCBS/man/ScanCBSSimPlot.Rd SeqCNVCBS/man/nhppSimConstWindowGen.Rd SeqCNVCBS/man/ScanIterateGrid.Rd SeqCNVCBS/man/JSSim_TumorSim1.Rd SeqCNVCBS/man/nhppSimConstWindow.Rd SeqCNVCBS/man/JSSim_SpikeMat.Rd SeqCNVCBS/man/readInput.Rd SeqCNVCBS/man/ScanStatRefineComp.Rd SeqCNVCBS/man/JSSim_NormalSim1.Rd SeqCNVCBS/man/ScanCBSPlot.Rd SeqCNVCBS/man/readSeqJShen.Rd
SeqCNVCBS/src
SeqCNVCBS/src/seqCNVCBS.c

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