ade4 (version 1.7-8)

fuzzygenet: Reading a table of genetic data (diploid individuals)

Description

Reads data like char2genet without a priori population

Usage

fuzzygenet(X)

Arguments

X

a data frame of strings of characters (individuals in row, locus in variables), the value coded '000000' or two alleles of 6 characters

Value

returns a data frame with the 6 following attributs:

col.blocks

a vector containing the number of alleles by locus

all.names

a vector containing the names of alleles

loc.names

a vector containing the names of locus

row.w

a vector containing the uniform weighting of rows

col.freq

a vector containing the global allelic frequencies

col.num

a factor ranking the alleles by locus

Details

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 carying alleles 012 and 028; 020020 for a homozygote carrying two alleles 020 and 000000 for a not classified locus (missing data).

In exit, a fuzzy array with the following encoding for a locus: 0 0 1 … 0 for a homozygote 0 0.5 0.5 … 0 for a heterozygote p1 p2 p3 … pm for an unknown where (p1 p2 p3 … pm) is the observed allelic frequencies for all tha available data.

References

~put references to the literature/web site here ~

See Also

char2genet if you have the a priori definition of the groups of individuals (populations). It may be used on the created object dudi.fca

Examples

# NOT RUN {
data(casitas)
casitas[1:5, ]
casitas <- fuzzygenet(casitas)
attributes(casitas)
rm(casitas)
# }