simPCR2: Polymorphism chain reaction simulation model
In forensim: Statistical tools for the interpretation of forensic DNA mixtures

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

simPCR2 implements a simulation model for the polymorphism chain reaction (Gill et al., 2005). Giving several input parameters, simPCR2 outputs the number of amplified DNA molecules and their corresponding peak heights (in RFUs).

1 2	simPCR2(ncells,probEx,probAlq, probPCR, cyc = 28, Tdrop = 2 * 10^7, probSperm = 0.5, dip = TRUE,KH=55)

`ncells`	initial number of cells
`probEx`	probability that a DNA molecule is extracted (probability of surviving the extraction process)
`probAlq`	probability that a DNA molecule is selected for PCR amplification
`probPCR`	probability that a DNA molecule is amplified during a given round of PCR
`cyc`	number of PCR cycles, default is 28 cycles
`Tdrop`	threshold of detection: number of molecules (in the total PCR reaction mixture) that is needed to generate a signal, default is set to 2*10^7 molecules
`probSperm`	probability of observing alleles of type A in the initial sample of haploid cells (e.g. sperm cells). Probability of observing allele B is given by 1-`probSperm`
`dip`	logical indicating the cell ploidy, default is diploid cells (TRUE), FALSE is for haploid cells
`KH`	positive constant used to scale the peak heights obtained from the number of amplified molecules (see reference section)

A threshold of Tdrop (must be a multiple of 10^7) is needed to generate a signal, then, a log-linear relationship is used to determine the intensity of the signal with respect to the number of successfully amplified DNA molecules. Dropout events occur whenever less than Tdorp molecules are generated.

A matrix with the following components:

`HeightA`	Peak height of allele A
`DropA`	Dropout variable for allele A
`HeightB`	Peak height of allele B
`DropB`	Dropout variable for allele B

Hinda Haned contact@hindahaned.info

Jeffreys AJ, Wilson V, Neumann R and Keyte J. Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells. Nucleic Acids Res 1988;16: 10953_10971.

Gill P, Curran J and Elliot K. A graphical simulation model of the entire DNA process associated with the analysis of short tandem repeat loci. Nucleic Acids Research 2005, 33(2): 632-643.

simPCR2TK

1 2	#simulation of a 28 cycles PCR, with the initial stain containing 5 cells simPCR2(ncells=5,probEx=0.6,probAlq=0.30,probPCR=0.8,cyc=28, Tdrop=2*10^7,dip=TRUE,KH=55)