Polymorphism chain reaction simulation model

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Description

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).

Usage

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

Arguments

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)

Details

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.

Value

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

Author(s)

Hinda Haned contact@hindahaned.info

References

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.

See Also

simPCR2TK

Examples

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#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)

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