I have browsed the manual but I couldn't find how to calculate metrics of differentiation in poppr , and poppr.amova() is also not applicable for snpclone object. Is there a way to solve it ?
Moreover, If I want to export my snpclone object which is MLG filtered, how should I code?
On Jan 23, 2018, at 08:51 , Yu NING <ningy...@qq.com> wrote:
Hi~I have browsed the manual but I couldn't find how to calculate metrics of differentiation in poppr , and poppr.amova() is also not applicable for snpclone object. Is there a way to solve it ? Moreover, If I want to export my snpclone object which is MLG filtered, how should I code? Thanks very much
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> Blygl_dis<- bitwise.dist(Bly_gl, percent = FALSE)> Bly_amova<- pegas::amova(Blygl_dis ~ pop, data = strata(Bly_gl), is.squared = TRUE)Error in FUN(X[[i]], ...) : 'bin' must be numeric or a factorIn addition: Warning message:In pegas::amova(Blygl_dis ~ pop, data = strata(Bly_gl), is.squared = TRUE) : elements in the rhs of the formula are not all factors
> Bly_gl /// GENLIGHT OBJECT /////////
// 39 genotypes, 7,227 binary SNPs, size: 969.5 Kb 11255 (3.99 %) missing data
// Basic content @gen: list of 39 SNPbin @ploidy: ploidy of each individual (range: 2-2)
// Optional content @ind.names: 39 individual labels @loc.names: 7227 locus labels @chromosome: factor storing chromosomes of the SNPs @position: integer storing positions of the SNPs @pop: population of each individual (group size range: 2-3) @other: a list containing: elements without names
popslot_Kob<-pop(Kob_snpclo)
Blygl_dis<- bitwise.dist(Bly_gl, percent = FALSE)
Bly_amova<- pegas::amova(Blygl_dis ~ popslot, data = strata(Bly_gl), is.squared = TRUE)
Bly_amova<- pegas::amova(Blygl_dis ~ pop, data = strata(Bly_gl), is.squared = TRUE)
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popslot<-pop(Bly_snpclo)
Blygl_dis<- bitwise.dist(Bly_gl, percent = FALSE)Bly_amova<- pegas::amova(Blygl_dis ~ popslot, data = strata(Bly_gl), is.squared = TRUE)
Bly_amova
Analysis of Molecular Variance
Call: pegas::amova(formula = Blygl_dis ~ popslot, data = strata(Bly_gl), is.squared = TRUE)
SSD MSD dfpopslot 40434.10 3110.316 13Error 36754.33 1470.173 25Total 77188.44 2031.275 38
Variance components: sigma2 P.valuepopslot 589.75 0.048Error 1470.17
Variance coefficients: a 2.781065
Hello,
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