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 <[email protected]> > 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 <[email protected]> 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 >> > _______________________________________________ R-sig-genetics mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
