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fuzzygenet 105
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
Details
Value
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.
returns a data frame with the 6 following attributs:
col.blocks
all.names
loc.names
row.w
col.freq
col.num
a vector containing the number of alleles by locus
a vector containing the names of alleles
a vector containing the names of locus
a vector containing the uniform weighting of rows
a vector containing the global allelic frequencies
a factor ranking the alleles by locus
Note
In the exit data frame, the alleles are numbered 1, 2, 3, . . . by locus and the loci are called L01, L02,
L03, . . . for the simplification of listing. The original names are kept.
Author(s)
Daniel Chessel