[R-sig-genetics] genlight to genind conversion

[Daniel Fulop]

Hi Zhian,

Thanks a ton!  That is super helpful.

I’m also looking to bootstrap a Nei’s distance NJ tree, and I see that I can do that with about().

All the best,
Dan.


> On Nov 16, 2015, at 9:20 PM, Zhian Kamvar <kamvarz at science.oregonstate.edu> wrote:
> 
> Hi Dan,
> 
> The question of how to analyze genomic SNP data in poppr was recently addressed:
> https://groups.google.com/forum/#!topic/poppr/_0GWvgC85S8
> 
> What functions related to clonal and mixed reproduction are you looking to utilize? Adegenet has several functions for use with genlight objects including DAPC and PCA. Additionally, poppr v2 has the ability to perform the index of association and all multilocus genotype functions on genlight objects. 
> 
> Otherwise, a genlight to genind conversion usually takes the form of:
> 
> x.mat <- as.matrix(x) # x is a genlight object
> x.mat[x.mat == 0] <- "1/1" # homozygote reference
> x.mat[x.mat == 1] <- "1/2" # heterozygote
> x.mat[x.mat == 2] <- "2/2" # homozygote alternate
> x.gid <- df2genind(x, sep = "/", ploidy = 2)
> 
> The object you get back will be ~55Mb
> 
> I hope that addressed some of your questions.
> 
> Best,
> Zhian
> 
>> On Nov 16, 2015, at 20:55 , Daniel Fulop <dfulop.ucd at gmail.com> wrote:
>> 
>> 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
>> 
>