Hi Zhian, I’m glad I asked! The StAMPP package can calculate Nei’s distance on a genlight object using the stamppNeisD() function. I thought of coding the resampling myself, but if I can incorporate stamppNeisD() within aboot() that’ll save me some trouble.
Any thoughts about hacking aboot() to use stamppNeisD()? Thanks again! Dan. > On Nov 16, 2015, at 10:03 PM, Zhian Kamvar <[email protected]> > wrote: > > Hi Dan, > > There is a slight catch to this: > > Bootstrapping for genlight objects defaults to a simple measure of > dissimilarity (see the function bitwise.dist). To use Nei's distance, you > must convert to either genind or genpop (unless you want to write the > function to calculate Nei's distance off of a genlight object). > > Zhian > > >> On Nov 16, 2015, at 21:32 , Daniel Fulop <[email protected]> wrote: >> >> 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
