sim_dpcr: Simulate Droplet Digital PCR
In dpcR: Digital PCR Analysis

Description Usage Arguments Details Value Note Author(s) See Also Examples

A function that simulates results of a droplet digital PCR.

1 2	sim_dpcr(m, n, times, n_exp = 1, dube = FALSE, pos_sums = FALSE, fluo = NULL)

`m`	the total number of template molecules used in the expertiment. Must be a positive integer.
`n`	the number of droplets per experiment. Must be a positive integer.
`times`	number of repetitions (see Details).
`n_exp`	the number of experiments that are simulated by the function. Cannot have higher value than the `times` argument.
`dube`	if `TRUE`, the function is strict implementation of digital PCR simulation (as in Dube et al., 2008). If `FALSE`, the function calculates only approximation of Dube's experiment. See Details and References.
`pos_sums`	if `TRUE`, function returns only the total number of positive (containing at least one molecule) chamber per panel. If `FALSE`, the functions returns a vector of length equal to the number of chambers. Each element of the vector represents the number of template molecules in a given chamber.
`fluo`	if `NULL`, the function calculates number of molecules per well or total number of positive droplets. If list of two, the first argument defines smoothness of the fluorescence curve and second space between two consecutive measured droplets. Space must be a vector containing positive integers of the length `n` or 1.

The function contains two implementations of the array digital PCR simulation. First one was described in Dube at. al (2008). This method is based on random distributing m * times molecules between n * times chambers. After this step, the required number of plates is created by the random sampling of chambers without replacement. The above method is used, when the dube argument has value TRUE.

The higher the value of the argument times, the simulation result is closer to theoretical calculations.

If the pos_sums argument has value FALSE, the function returns matrix with n rows and n_panels columns. Each column represents one plate. The type of such simulation would be "nm". If the pos_sums argument has value TRUE, the function return matrix with one row and n_panels columns. Each column contains the total number of positive chambers in each plate and type of simulation would be set as "tnp".

In each case the value is an object of the dpcr class.

Although Dube's simulation of digital PCR was developed for array digital PCR, it's also viable for simulating droplet-based methods.

Michal Burdukiewicz, Stefan Roediger.

sim_adpcr.

#simulate fluorescence data
tmp_VIC <- sim_dpcr(m = 7, n = 20, times = 5, fluo = list(0.1, 0))
tmp_FAM <- sim_dpcr(m = 15, n = 20, times = 5, fluo = list(0.1, 0))
par(mfrow = c(2,1))
plot(tmp_VIC, col = "green", type = "l")
plot(tmp_FAM, col = "blue", type = "l")
summary(tmp_FAM)

summary(sim_dpcr(m = 7, n = 20, times = 5, n_exp = 5))