nhppSimConstWindowGen: Simulate a Non-Homogeneous PP with constant window spike
In SeqCNVCBS: Scan Statistics for CNV Detection with CBS

Description Usage Arguments Details Value Author(s) See Also

Simulate non-homogeneous Poisson processes with a number of constant-widths windows of signal spike, and output the data and meta file

1	nhppSimConstWindowGen(controlRates, filename, chromosomeN, nSpike=25, cptLen=c(3,5,8,12,20,30,50,75,100), nPair=2, nRepeat=10, minGain=1.5, maxGain=4, minLoss=0.01, maxLoss=0.5, pGain=0.6)

`controlRates`	The estimated rate of nhpp for the control
`filename`	The prefix of all the output files from this simulation
`chromosomeN`	The chromosome number. Should be the number from which the samples are emulated
`nSpike`	Number of signal spikes
`cptLen`	Constant width of the signal (CN gain or loss) region to simulate, can be a vector of different values for which to test
`nPair`	Number of tumor samples to generate for each choice of the width of the signal; number of normal samples to generate
`nRepeat`	Number of times to repeat the simulation data generation
`minGain`	Minimal signal gain
`maxGain`	Maximal signal gain
`minLoss`	Minimal signal loss
`maxLoss`	Maximal signal loss
`pGain`	Proportion of the signal regions that are CN gain

This function is used in conjunction with a modified, windowed rate vector to simulate non-homogeneous Poisson processes with a number of constant-widths windows of signal spike. One should use the nhppRateEstimate function to estimate the rate of a control sample one wishes to mimic. This function randomly choose windows of a specified constant width, and spike in signals (change points) which can be either gain or loss of copy numbers.

No return value. Generates a number of .txt files, one for each normal/tumor sample as raw data, one input meta file and a file with the true change points for each choice of cptLen.

Jeremy J. Shen

nhppSimulate

SeqCNVCBS documentation built on May 2, 2019, 6:51 p.m.