Hi Zhian, Thanks again!!
Best, Dan. > On Nov 16, 2015, at 10:30 PM, Zhian Kamvar <[email protected]> > wrote: > > Hi Dan, > > Thanks for pointing that out! It can't be calculated in poppr as it exists on > CRAN, but I just pushed a fix for aboot on github that will allow you to use > any distance metric with genlight objects (previously, it would force > bitwise.dist). > > you can install it with devtools::install_github("grunwaldlab/poppr@devel") > > I would also recommend installing the github versions of adegenet and pegas. > > Here's an example of bootstrapping with StAMPP: > > library(poppr) > library(StAMPP) > x <- glSim(100, 1e3, ploid=2) > pop(x) <- rep(LETTERS[1:5], 20) > aboot(x, distance = function(x) as.dist(stamppNeisD(x)), sample = 100) > > Best, > Zhian > > >> On Nov 16, 2015, at 22:11 , Daniel Fulop <[email protected]> wrote: >> >> 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
