[adegenet-forum] problem to import data with read.structure
stephanie.manel at ujf-grenoble.fr
Wed Jul 23 09:26:58 CEST 2008
My question is about the data importation and the use of read.structure
In the tutorial I read:
"In all cases, it should be possible to store data in an individuals x
markers table where each element is a character string coding 2 alleles
Such data are interpretable when all strings contain 2,4 or 6 characters."
In my case the allele are not stored together and should *not be
coded with two character(*s)?
In more detail:
In fact I have a problem for importing data with adegent using
read.structure (which is the most convenient when the two alleles of
each loci are not stored together but in two different colon). When in
my data to import, I have allele coded with 2 and 1 characters , I have
no probleme to import the data. However when I have all the alleles
coded with only one characters, I cannot import the file and I have the
following error message:
_I used the following command:_
Error in df2genind(X = X, pop = pop, missing = missing) :
Invalid number of coding characters (should be 2, 4, or 6)
_My questions are:_
- is the error message due to the fact that the alleles are coded with
only one character?
-when in a dataset alleles are coded with two and one character, R read
all with two characters?
-what is the best way to import such data (file text with allele not
-one allele is coded by 0 : is it a problem ?
Thank you for your attention
Université Joseph Fourier,
Laboratoire d'Ecologie Alpine, Equipe GPB
UMR-CNRS 5553, BPX53 Grenoble 38041
tél: 04 76 51 41 15
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