make_dummy {freqpcr}

Generate dummy DNA dataset ready for allele-frequency estimation.

Description

The function generates a dummy dataset of typical RED-\Delta\DeltaCq analysis. You can directly feed the output of this function to the first argument of sim_dummy().

Usage

make_dummy(
  rand.seed,
  P,
  K,
  ntrap,
  npertrap,
  scaleDNA = (1/K) * 1e-06,
  targetScale,
  baseChange,
  EPCR,
  zeroAmount,
  sdMeasure,
  diploid = FALSE
)

Arguments

rand.seed

Seed for the R built-in random-number-generator.

P

A numeric between 0 and 1 giving the population allele frequency from which the test samples are generated.

K

A positive numeric of the gamma shape parameter of the individual DNA yield.

ntrap, npertrap

Scalar specifying the number of bulk samples (ntrap) and the numbers of individuals contained in each bulk sample (npertrap). Currently limited to the cases that all bulk samples have the same sample size: e.g. (4 + 4 + 4) when ntrap = 3 and npertrap = 4 hold.

scaleDNA

Small positive scalar that specifies the scale parameter of the gamma distribution appriximating the DNA yield from (per-haploid) individual. The yield of 2*scaleDNA is expected from a diploid. The quantity is determined as the relative amount, in linear scale, to the termination threshold of the real-time PCR.

targetScale

(\delta_{T}) The relative template DNA amount of the target gene to the houskeeping gene, given as a positive numeric.

baseChange

(\delta_{B}) The change rate in the template DNA quantities after the restriction enzyme digestion (in the RED-\Delta\DeltaCq method), given as a positive numeric. This parameter is not used in freqpcr().

EPCR

(\eta) Amplification efficiency per PCR cycle, given as a positive numeric. When EPCR = 1, template DNA doubles every cycle (EPCR + 1 = 2).

zeroAmount

A numeric between 0 and 1, usually near 0, giving the residue rate of restriction enzyme digestion in RED-\Delta\DeltaCq method.

sdMeasure

(\sigma_{c}) Scalar. The measurement error (standard deviation) on each Cq value following Normal(0, \sigma_{c}^2). If known, given as a positive numeric.

diploid

Is the target organism diploidy? Default is FALSE, assuming haploidy. Current implementation of diploidy assumes i.i.d. between the amounts of R and S chromosomes owned by a heterozygote individual, which is unlikely in many animals but necessary for the calculation in a realistic time.

Value

Object of the S4 class CqList, storing the dummy experiment data of Cq-based qPCR analysis. Note that a CqList object in no way contains original information on P, K, targetScale, sdMeasure, and EPCR.

Examples

P <- 0.25
# Just a test: segregation ratios for six bulk samples, 1000 individuals for each.
rmultinom(n=6, size=1000, prob=c(P, 1-P)) # haploidy
rmultinom(6, size=1000, prob=c(P^2, 2*P*(1-P), (1-P)^2)) # diploidy

# Dummy Cq dataset with six bulk samples, each of which comprises eight haploids.
dmy_cq <- make_dummy( rand.seed=1, P=0.15, K=2, ntrap=6, npertrap=8,
                      scaleDNA=1e-07, targetScale=1.5, baseChange=0.3, EPCR=0.95,
                      zeroAmount=1e-3, sdMeasure=0.3, diploid=FALSE )
print(dmy_cq)