[adegenet-forum] Looking for help with a PCA using adegenet in R

[Sarrah Castillo]

Hello Dr. Jombart
I was wondering if you could help me with an issue I am having with your program (Adegenet) in R.
I am attempting to perform a PCA using a structure file. The difference is that this is based on tetraploid data.  Structure allows for multiple ploidy, however I am unsure of how to have the program read my data as tetraploid instead of diploid. The genetic information is for a single locus with between 2-4 alleles (with -9 representing missing data)

Here is an example of my file (with -9 representing missing data)

Ind	Reg	Al1	Al2	Al3	Al4
271	ON	7	10	11	-9
273	ON	2	10	13	-9
272	ON	4	11	12	-9
465	ON	1	2	-9	-9
472	ON	3	6	11	19
489	ON	2	3	4	19
519	ON	7	12	-9	-9
551	ON	7	14	43	-9
466	ON	4	5	15	19
749	ON	7	14	20	26
111	ON	5	7	8	-9
173	ON	4	11	21	-9
318	ON	7	21	24	-9
319	ON	1	20	26	49
323	ON	7	16	20	26
341	ON	7	25	27	49
385	ON	3	19	25	49
485	ON	7	9	12	-9

Ind=individual
Reg=region
Al1= allele 1
Al2= allele 2
Al3= allele 3
Al4= allele 4


Any help would be much appreciated.

Thank you
Sarrah Castillo


____________________
Sarrah Castillo
MSc Candidate
Environmental & Life Sciences Graduate Program
Trent University, 2140 East Bank Drive, 
Peterborough, Ontario, K9J 7B8, Canada
e-mail:scastillo at nrdpfc.ca

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20101019/3db72e40/attachment.htm>