nhppSimConstWindow: 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 run CBS on them.

1	nhppSimConstWindow(controlRates, nSpike = 25, cptLen = seq(5, 50, by = 5), nRepeat = 5, minGain = 1.5, maxGain = 5, minLoss = 0.01, maxLoss = 0.5, pGain = 0.6)

`controlRates`	The estimated rate of nhpp for the control
`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
`nRepeat`	Number of total samples to generate for each choice of the width of the signal
`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, and run CBS on them. 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.

Return the results of the simulation in a list

Jeremy J. Shen

nhppSimulate

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