The ade4 Package - NexTag Supports Open Source Initiatives

108 genet
Description
There are multiple formats of genetic data. The functions of ade4 associated genetic data use the
class genet. An object of the class genet is a list containing at least one data frame whose
lines are groups of individuals (populations) and columns alleles forming blocks associated with
the locus. They contain allelic frequencies expressed as a percentage.
The function char2genet ensures the reading of tables crossing diploid individuals arranged by
groups (populations) and polymorphic loci. Data frames containing only strings of characters are
transformed in tables of allelic frequencies of the class genet. In entry a row is an individual, a
variable is a locus and a value is a string of characters, for example ’ 012028 ’ for a heterozygote
carrying alleles 012 and 028, ’ 020020 ’ for a homozygote carrying two alleles 020 and ’ 000000 ’
for a not classified locus (missing data).
The function count2genet reads data frames containing allelic countings by populations and
allelic forms classified by locus.
The function freq2genet reads data frames containing allelic frequencies by populations and
allelic forms classified by locus.
In these two cases, use as names of variables of strings of characters xx.yyy where xx are the
names of locus and yyy a name of allelic forms in this locus. The analyses on this kind of data
having to use compact labels, these functions classify the names of the populations, the names of
the loci and the names of the allelic forms in vectors and re-code in a simple way starting with P for
population, L for locus and 1,. . . , m for the alleles.
Usage
char2genet(X, pop, complete)
count2genet(PopAllCount)
freq2genet(PopAllFreq)
Arguments
X
pop
complete
PopAllCount
PopAllFreq
a data frame of strings of characters (individuals in row, locus in variables), the
value coded ’000000’ or two alleles of 6 characters
a factor with the same number of rows than df classifying the individuals by
population
a logical value indicating a complete issue or not, by default FALSE
a data frame containing integers: the occurrences of each allelic form (column)
in each population (row)
a data frame containing values between 0 and 1: the frequencies of each allelic
form (column) in each population (row)
Details
As a lot of formats for genetic data are published in literature, a list of class genet contains at
least a table of allellic frequencies and an attribut loc.blocks. The populations (row) and the
variables (column) are classified by alphabetic order. In the component comp, each individual per
locus of m alleles is re-coded by a vector of length m: for hererozygicy 0,. . . ,1,. . . ,1,. . . ,0 and
homozygocy 0,. . . ,2,0.