Fits models for genotypic disequilibria, as described in Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986).
hwde(data = IndianIrish, gp = "Population", termlist = NULL, refmodel = NULL, loci = paste("locus", 1:(dim(data)[2] - 1), sep = ""), observed = "Observed", keep.models = FALSE, aovtable.print = TRUE, group.terms = TRUE, allele.chars = letters)
data |
Must have a column of frequencies, by default called
Observed , and one or more columns giving genotype
information,
in the form AA, Aa, aa. or e.g., MM, MN, NN. (The choice of letters
is arbitrary.) Additionally, there may be a column that gives
information on groupings, by default called Population .
|
gp |
Gives the name of the column, if any, that has information on groups within the data. |
termlist |
Use to specify a user-defined sequence of models. See the vignette hwde.pdf or hwde.html |
refmodel |
For each model in termlist , specifies a
reference model, which will be updated to include the additional terms. |
loci |
Gives name(s) of columns that hold information on
genotypes. By default, these are taken to be locus1 ,
locus2 , etc. |
observed |
Name (by default Observed ) of the column that
holds the frequenceies. |
keep.models |
Should a list be returned that holds the full sequence of models that were fitted? |
aovtable.print |
Should the anova table be printed? |
group.terms |
Should model terms be grouped according to hierarchy, for the anova table? |
allele.chars |
A sequence of letters used to code for the loci. By default em{a}, em{b}, em{c}, ... are used |
See the document hwde.pdf or hwde.html for details. See the references (below) for information on the interpretation of model parameters.
anovatab |
anova (analysis of deviance) table |
data.df |
Data, and contrasts used in fitting the various models. |
aovtab.terms |
This string holds, for each model that is
fitted. the terms that have appeared in the model formula.
The text strings for the distinct models are concatenated.
|
references{
1. Huttley, G.A. and Wilson, S.R. 2000. Testing for concordant
equilibria between population samples. Genetics 156:2127-2135.
2. Weir, B.S. 1996. em{Genetic Data Analysis II.} Sinauer.
3. Weir, B.S. and Wilson, S.R. 1986. Log-linear models for
linked loci. em{Biometrics} 42:665-670.
}
author{J.H. Maindonald}
seealso{make.contrasts
, identify.genotypes
}
examples{
data(IndianIrish)
hwde(data=IndianIrish}
data(mendel3)
hwde(data=mendel3
J.H. Maindonald
1. Huttley, G.A. and Wilson, S.R. 2000. Testing for concordant
equilibria between population samples. Genetics 156:2127-2135.
2. Weir, B.S. 1996. em{Genetic Data Analysis II.} Sinauer.
3. Weir, B.S. and Wilson, S.R. 1986. Log-linear models for
linked loci. em{Biometrics} 42:665-670.
make.contrasts
, identify.genotypes
data(IndianIrish) hwde(data=IndianIrish