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
