Description Usage Arguments Value Author(s) See Also Examples
Simulate some data for a slab gel.
1 2 3 4 5 6 | 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"))
|
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 ( |
An AFLP object with dummy fluoresence data. The fluorescence slot has an extra binary variable "Truth".
Thierry Onkelinx Thierry.Onkelinx@inbo.be, Paul Quataert
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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"
)
|
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