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

Functions

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
nhppSimConstWindow Man page
nhppSimConstWindowAnalysis Man page
nhppSimConstWindowGen Man page
nhppSimulate Man page
nhppSpike Man page
nhppSpikeConstSignal Man page
nhppSpikeConstWindow Man page
readInput Man page
readListInputFile Man page
readSeq Man page
readSeqChiang Man page
readSeqELANDPaired Man page
readSeqJShen Man page
readSeqMLove 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
SeqCNVCBS Man page
SeqCNVCBS-package Man page

Files

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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