amova analysis by VCF file

[duguyiw...@163.com]

dear poppr support：

    I have a vcf file and group list，when I want to analysis amova，it turns out NaN result I want to know why？

My code is

library("poppr")

library("vcfR")

vcf<-read.vcfR("/mnt/ilustre/users/tong.wang/Project/MJ20180320018-yaozhangxiu/evo20180814/step01.vcf-filter/pop.recode.vcf")

popdata<-read.table("/mnt/ilustre/users/tong.wang/Project/MJ20180320018-yaozhangxiu/group.list")

colnames(popdata)<-c("sampleID","groupID") # groupID i

g<-vcfR2genind(vcf)

g<-as.genclone(g)

ploidy(g)<-2

strata(g)<-data.frame(popdata)

setPop(g)<-~groupID

pop<-poppr(g)

amovacc<-poppr.amova(g3,~sampleID/groupID,clonecorrect=TRUE)

I wander know why and how to fix it？

thank you！

[Zhian Kamvar]

Hi,

The problem is that you are defining your samples as a hierarchical level. You should only need to specify ~groupID as the hierarchy in your AMOVA. If you have diploid individuals, poppr will calculate within-individual variance automatically with no need to specify that as part of the hierarchy.

hope that helps,

Zhian

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[Zhian Kamvar]

I'm going to post a reproduction of this situation here in case anyone ends up with the same error:

suppressPackageStartupMessages(library(poppr))
data(nancycats)
strata(nancycats) <- data.frame(POP = pop(nancycats), ID = indNames(nancycats))
poppr.amova(nancycats, ~POP/ID, quiet = TRUE)
#> Warning in is.euclid(xdist): Zero distance(s)
#> Distance matrix is non-euclidean.
#> Using quasieuclid correction method. See ?quasieuclid for details.
#> Warning in is.euclid(distmat): Zero distance(s)
#> $call
#> ade4::amova(samples = xtab, distances = xdist, structures = xstruct)
#>
#> $results
#>                            Df    Sum Sq   Mean Sq
#> Between POP                16  288.5021 18.031384
#> Between ID Within POP     220 1235.8990  5.617723
#> Between samples Within ID   0    0.0000       NaN
#> Within samples            237 1015.6256  4.285340
#> Total                     473 2540.0268  5.370035
#>
#> $componentsofcovariance
#>                                         Sigma   %
#> Variations  Between POP                   NaN NaN
#> Variations  Between ID Within POP         NaN NaN
#> Variations  Between samples Within ID     NaN NaN
#> Variations  Within samples            4.28534 NaN
#> Total variations                          NaN NaN
#>
#> $statphi
#>                   Phi
#> Phi-samples-total NaN
#> Phi-samples-ID    NaN
#> Phi-ID-POP        NaN
#> Phi-POP-total     NaN

Created on 2018-09-04 by the reprex package (v0.2.0).

[duguyiw...@163.com]

thanks for your reply soon thank you！

but Why My result is different between nanycat？

like

but Mine is

is there somethin I have missed？

thankyou！

在 2018年9月4日星期二 UTC+8下午6:23:51，Zhian Kamvar写道：

[duguyiw...@163.com]

by the way

all report about my data is:

thank you

在 2018年9月4日星期二 UTC+8下午6:55:12，duguyiw...@163.com写道：

[duguyiw...@163.com]

I have already fix it by another way like this

library(pegas)

library(adegenet)

library(poppr)

info <- VCFloci("pop.recode.vcf")

popdata<-read.table("group.list")

SNP <- is.snp(info)

x <- length(which(SNP))

x <- read.vcf("amova/pop.recode.vcf", from = 1, to = x)

g<-loci2genind(x)

g<-as.genclone(g)

ploidy(g)<-2

strata(g)<-data.frame(popdata)

amovacc<-poppr.amova(g,~groupID/sampleID,dist=x.dist)

maybe loci2genind is different from vcfR2genind

thankyou！

在 2018年9月4日星期二 UTC+8下午6:23:51，Zhian Kamvar写道：

I'm going to post a reproduction of this situation here in case anyone ends up with the same error: