Simulate non-homogeneous Poisson processes with a number of constant-widths windows of signal spike, and output the data and meta file
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)The estimated rate of nhpp for the control
The prefix of all the output files from this simulation
The chromosome number. Should be the number from which the samples are emulated
Number of signal spikes
Constant width of the signal (CN gain or loss) region to simulate, can be a vector of different values for which to test
Number of tumor samples to generate for each choice of the width of the signal; number of normal samples to generate
Number of times to repeat the simulation data generation
Minimal signal gain
Maximal signal gain
Minimal signal loss
Maximal signal loss
Proportion of the signal regions that are CN gain
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.
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.