nhppSimConstWindowGen {seqCBS} | R Documentation |
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)
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