HWE.test is a generic function to
perform Hardy-Weinberg Equilibrium tests defined by the
genetics package. adegenet proposes a method for
The output can be of two forms:
- a list of tests (class
htest) for each locus-population
- a population x locus matrix containing p-values of the tests
an object of class
a factor giving the population of each individual. If NULL, pop is seeked from x\$pop.
a logical passed to
number of simulations if Monte Carlo is used (passed to
a logical stating whether non-tested loci (e.g., when an allele is fixed) should be hidden in the results (TRUE, default) or not (FALSE).
a character or a character vector whose only first argument is considered giving the type of result to display. If "full", then a list of complete tests is returned. If "matrix", then a matrix of p-values is returned.
Monte Carlo procedure is quiet computer-intensive when large
datasets are involved. For more precision on the performed test, read
HWE.test documentation (
Returns either a list of tests or a matrix of p-values. In the
first case, each test is designated by locus first and then by
population. For instance if
res is the "full" output of the
function, then the test for population "PopA" at locus "Myloc" is
given by res$Myloc$PopA. If
res is a matrix of p-values,
populations are in rows and loci in columns. P-values are given for
the upper-tail: they correspond to the probability that an oberved
chi-square statistic as high as or higher than the one observed
occured under H0 (HWE).
In all cases, NA values are likely to appear in fixed loci, or entirely non-typed loci.
Thibaut Jombart firstname.lastname@example.org
1 2 3 4 5 6 7 8 9 10 11 12 13 14
Loading required package: ade4 /// adegenet 2.0.1 is loaded //////////// > overview: '?adegenet' > tutorials/doc/questions: 'adegenetWeb()' > bug reports/feature requests: adegenetIssues() Loading required package: genetics Loading required package: combinat Attaching package: 'combinat' The following object is masked from 'package:utils': combn Loading required package: gdata sh: 1: cannot create /dev/null: Permission denied gdata: Unable to locate valid perl interpreter gdata: gdata: read.xls() will be unable to read Excel XLS and XLSX files gdata: unless the 'perl=' argument is used to specify the location of a gdata: valid perl intrpreter. gdata: gdata: (To avoid display of this message in the future, please ensure gdata: perl is installed and available on the executable search path.) sh: 1: cannot create /dev/null: Permission denied gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLX' (Excel 97-2004) files. gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLSX' (Excel 2007+) files. gdata: Run the function 'installXLSXsupport()' gdata: to automatically download and install the perl gdata: libaries needed to support Excel XLS and XLSX formats. Attaching package: 'gdata' The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith Loading required package: gtools Attaching package: 'gtools' The following object is masked from 'package:adegenet': chr Loading required package: MASS Loading required package: mvtnorm NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced genetics packages to replace 'genetics'. Please visit the project homepage at http://rgenetics.org for informtion. Attaching package: 'genetics' The following objects are masked from 'package:base': %in%, as.factor, order As of adegenet_1.5-0, this function has been removed and is replaced by 'hw.test' in the package 'pegas' As of adegenet_1.5-0, this function has been removed and is replaced by 'hw.test' in the package 'pegas' NULL
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.