Copy Number Profiling using Sequencing and CBS

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Documentation for package ‘seqCBS’ version 1.2.1

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seqCBS-package Scan Statistics CNV detection using sequencing data
BayesCptCI Bayesian Point-wise Confidence Interval for Change-Point Model
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 length in each set
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 formats
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 Scan Statistics CNV detection using sequencing data