dummySlabgel: Simulate some data for a slab gel.

In AFLP: Analysis of AFLP data

Description

Simulate some data for a slab gel.

Usage

  dummySlabgel(nSpecimen = 50, nGroup = 2, nMarker = 50,
    nReplicate = 3,
    markerProb = c(Monomorph = 0.2, Group = 0.5),
    fixed = c(Intercept = 9, Score = 1.7, MarkerTrend = -0.007),
    betaShape = c(0.3, 0.8), VarCov,
    transformation = c("log", "logit", "none"))

Arguments

nSpecimen	The number of specimens. Defaults to 50.
nGroup	Number of a priori groups in the dataset. Defaults to 2.
nMarker	Number of markers in the dataset. Defaults to 50.
nReplicate	The number of specimens that are replicated on each plate. Defaults to 3.
markerProb	A named vector of length 2 with the probability that a marker is monomorph and the probability that a marker has a different proportion of presence between groups. Defaults to c(Monomorph = 0.2, Group = 0.5).
fixed	Overall mean fluorescence, overall difference in magnitude between present and absent bands and trend in fluorescence along the Defaults to c(Intercept = 9, Score = 1.7, MarkerTrend = -0.008).
betaShape	Shapeparameters of a beta distribution used to generate the probability that a marker is present. Defaults to c(0.3, 0.8).
VarCov	A list of variance covariance matrices of the specimens, replicates, markers, plates and noise. Defaults to list( Specimen = matrix(c(0.080, -0.017, -0.017, 0.025), ncol = 2), Replicate = matrix(c(0.116, -0.059, -0.059, 0.043), ncol = 2), Marker = matrix(c(0.581, -0.236, -0.236, 0.326), ncol = 2), Plate = matrix(c(0.154, -0.035, -0.035, 0.027), ncol = 2), Noise = 0.292 ).
transformation	Which transformation to use on the raw fluorescence data. Valid choises are "log", "logit" and "none". Defaults to "log". "log" implies the use of log(), hence no zero fluorescences are allowed. With "logit", the raw fluorescence is first devided by the smallest power of 2, which is still larger than the largest raw fluorescence. Then a logit transformation is applied (log(p/(1 - p))). Defaults to "log".

Value

An AFLP object with dummy fluoresence data. The fluorescence slot has an extra binary variable "Truth".

Author(s)

Thierry Onkelinx [e-mail], Paul Quataert

See Also

randomiseSlabgel, AFLP

Examples

dummy <- dummySlabgel(nSpecimen = 50, nGroup = 2, nMarker = 50,
   nReplicate = 3,
	  markerProb = c(Monomorph = 0.2, Group = 0.5),
	  fixed = c(Intercept = 9, Score = 1.7, MarkerTrend = -0.007),
	  betaShape = c(0.3, 0.8),
	  VarCov = list(
		  Specimen = matrix(c(0.080, -0.017, -0.017, 0.025), ncol = 2),
		  Replicate = matrix(c(0.116, -0.059, -0.059, 0.043), ncol = 2),
		  Marker = matrix(c(0.581, -0.236, -0.236, 0.326), ncol = 2),
		  Plate = matrix(c(0.154, -0.035, -0.035, 0.027), ncol = 2),
		  Noise = 0.292
	  ),
	  transformation = "log"
 )

AFLP documentation built on May 2, 2019, 6:13 p.m.