gwpcrpois: Poissonian Sampling Distribution of the PCR Product...

In Cibiv/gwpcR: Amplification+Sequencing Model Based on a Galton-Watson Branching Process and Poissonian Sampling

Description

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Usage

rgwpcrpois(
  n,
  efficiency,
  lambda0,
  threshold = 1,
  molecules = 1,
  method = NULL,
  cycles = Inf
)

dgwpcrpois(c, efficiency, lambda0, threshold = 1, molecules = 1)

pgwpcrpois(c, efficiency, lambda0, threshold = 1, molecules = 1)

Arguments

n	number of random samples to generate
efficiency	efficiency of amplification
lambda0	average number of observations per molecular family
threshold	minimal number of observations a molecular family must have to count as unambiguously detected. Setting this to a value v >= 0 conditions the distribution on c >= c, i.e every value of c less than that gets assigned probability zero.
molecules	initial copy number
method	the method used to draw from the PCR distribution. "simulate" simulates a Galton-Watson branching process modeling PCR, "gamma" uses approximates the PCR distribution with a Gamma distribution. By default, the Gamma approximation is used for small efficiencies, where it is quite good and where simulations are computationally expensive.
cycles	number of amplification cycles used for simulation. By default, a large enough value is used to make the results virtually idistinguishable from the limit for cycles \to ∞
c	number of observations of a particular molecular family

See Also

gwpcr

Cibiv/gwpcR documentation built on Aug. 31, 2021, 1:20 p.m.