sim_dummy: Simulate freqpcr estimation based on user-generated dummy...

In freqpcr: Estimates Allele Frequency on qPCR DeltaDeltaCq from Bulk Samples

Simulate freqpcr estimation based on user-generated dummy data.

Description

Wrapper of freqpcr() suitable for the performance test using a randomly-generated data object.

Usage

sim_dummy(
  CqList,
  EPCR,
  zeroAmount,
  P = NULL,
  K = NULL,
  targetScale = NULL,
  sdMeasure = NULL,
  beta,
  diploid,
  maxtime,
  print.level,
  aux = NULL,
  verbose = TRUE,
  ...
)

Arguments

CqList	Object belonging to the CqList class, typically the output from make_dummy(). Having the slots N, housek0, target0, housek1, and target1, all of which are numeric vectors of the same length.
EPCR	(η) 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-ΔΔCq method.
P, K, targetScale, sdMeasure	If NULL (default), the parameter is considered unknown and estimated via freqpcr(). If a value is specified, it is passed to freqpcr() as a fixed parameter. On the contrary, EPCR and zeroAmount are always treated as fixed parameters, for which values must be supplied.
beta, diploid, maxtime, print.level	Configuration parameters which are passed directly to freqpcr().
aux	Additional information to be displayed on the console. The default is NULL. If some value is input by the user, it is echoed to stdout together with the contents of the argument CqList. This option is convenient when you want to record the original dummy dataset and the corresponding result sequentially e.g. using capture.output().
verbose	Prints more information e.g. system time. Default is TRUE.
...	Additional arguments passed to freqpcr().

Value

Object of the S4 class CqFreq, which is same as freqpcr().

See Also

Other estimation procedures: freqpcr(), knownqpcr_unpaired(), knownqpcr()

Examples

# Prepare the parameter values.
K <- 2 # You already know the size of K in this case.
EPCR <- 0.97 # The sizes of EPCR and zeroAmount must always be supplied.
zeroAmount <- 1.6e-03
is.diploid <- FALSE

# First, make a dummy Cq dataset with six bulk DNA samples,
# each of which comprises of eight haploid individuals.
dmy_cq <- make_dummy( rand.seed=1, P=0.75, K=K, ntrap=6, npertrap=8, scaleDNA=1e-07,
                      targetScale=1.5, baseChange=0.3, EPCR=EPCR,
                      zeroAmount=zeroAmount, sdMeasure=0.3, diploid=is.diploid )

# Estimate the population allele frequency on the dummy dataset, presupposing K = 2.
sim_dummy(  CqList=dmy_cq, EPCR=EPCR, zeroAmount=zeroAmount,
            K=K,
            beta=TRUE, diploid=is.diploid, maxtime=60, print.level=2, aux="test" )

# If the maximum calculation time was too short to converge, nlm() returns error.
# Then sim_dummy() returns a matrix filled with zeros.
sim_dummy(  CqList=dmy_cq, EPCR=EPCR, zeroAmount=zeroAmount,
            beta=TRUE, diploid=is.diploid, maxtime=0.01, print.level=2 )

freqpcr documentation built on March 18, 2022, 7:25 p.m.