[R-sig-genetics] genlight to genind conversion

[Daniel Fulop]

Hi All,

I’d like to use adegenet and poppr to analyze RADseq SNP data from Aspen trees. I am limited in what I can do because I have not been able to convert my data from genlight to genind. At one point I tried, but then gave up because of the long computation time for the conversion I was attempting.

Is there a way to do the genlight to genind conversion? Otherwise, do you know if the functions related to clonal and mixed reproduction in poppr are implemented elsewhere (in R or outside of R)?

I know that genind objects are not efficient for storing SNP data.  For what it’s worth, we have 181 individuals and ~39000 SNPs.

Thanks advance for your help!
Dan.

-- 
Daniel Fulop, Ph.D.
Postdoctoral Scholar
Dept. Plant Biology, UC Davis
Maloof Lab, Rm. 2220
Life Sciences Addition, One Shields Ave.
Davis, CA 95616


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