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Dear all,<br>
<br>
My question is about the data importation and the use of read.structure
command.<br>
<br>
In the tutorial I read: <br>
"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<br>
Such data are interpretable when all strings contain 2,4 or 6
characters."<br>
<br>
In my case the allele are not stored together and should <b>not be
coded with two character(</b>s)? <br>
<br>
In more detail:<br>
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:<br>
<u>I used the following command:</u><br>
dataadegenet<-read.structure(nameoffilebis,n.ind=200,n.loc=20,
onerowperind=T,col.lab=1,col.pop=0,col.other=c(2,3),row.marknames=0,NA.char="-9")<br>
<u>Error message:</u><br>
Error in df2genind(X = X, pop = pop, missing = missing) : <br>
Invalid number of coding characters (should be 2, 4, or 6)<br>
<br>
<u>My questions are:</u><br>
- is the error message due to the fact that the alleles are coded with
only one character?<br>
-when in a dataset alleles are coded with two and one character, R read
all with two characters?<br>
-what is the best way to import such data (file text with allele not
together?)<br>
-one allele is coded by 0 : is it a problem ?<br>
<br>
Thank you for your attention<br>
Stéphanie<br>
<br>
<br>
<br>
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___________________________________<br>
Stéphanie Manel<br>
Université Joseph Fourier,<br>
Laboratoire d'Ecologie Alpine, Equipe GPB<br>
UMR-CNRS 5553, BPX53 Grenoble 38041<br>
tél: 04 76 51 41 15<br>
<a class="moz-txt-link-freetext" href="http://www-leca.ujf-grenoble.fr/membres/manel.htm">http://www-leca.ujf-grenoble.fr/membres/manel.htm</a><br>
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