Hi Ramendra, > Warning message: > In pegas::amova(amova_dist ~ Pop, data = amova_stra, nperm = 0) : > at least one missing value in the distance object.
This warning is most likely caused by having genotypes with reciprocal missing data, which result in a distance matrix with missing data. You have two options: 1. Interpolate the missing data in the distance matrix with the ape functions additive() or ultrametric() (see: http://stackoverflow.com/a/34022156/2752888 <http://stackoverflow.com/a/34022156/2752888> and http://dx.doi.org/10.1093/bioinformatics/bth211). 2. Find the genotypes that have the most incompatibilities (you can use the poppr function incomp() for this) and remove them. Hope that helps, Zhian > On Jan 2, 2017, at 01:37 , Ramendra Nath Sarma <[email protected]> wrote: > > Hi, > I used a file converted from Structure to use Pegas to analysis AMOVA and > to analyse Fst or other population parameters. Iam getting the error with > NA as: > Warning message: > In pegas::amova(amova_dist ~ Pop, data = amova_stra, nperm = 0) : > at least one missing value in the distance object. >> pegas_amova > > Analysis of Molecular Variance > > Call: pegas::amova(formula = amova_dist ~ Pop, data = amova_stra, nperm = 0) > > SSD MSD df > Pop NA NA 2 > Error 16241.53 113.5772 143 > Total NA NA 145 > > Variance components: > Pop Error > NA 113.5772 > > Variance coefficients: > a > 29.23973 > > > > My scripts in R as follows: > library("poppr") > library("adegenet") > amova<-read.structure ("~/Desktop/HARENDRA/structure1.str") > strata(amova) <- data.frame(Pop = pop(amova)) > library(pegas) > amova_dist <- dist(amova) # Euclidean distance > amova_dist > amova_stra <- strata(amova) > amova_stra > pegas_amova <- pegas::amova(amova_dist ~Pop, data = amova_stra, nperm = 0) > pegas_amova > > > Where I am wrong? Please suggest as novice to R. > > > ---------------------------------------------------------------------------------------------------------------------------------------- > > > > > > > *Dr R N SarmaProfessorDepartment of Plant Breeding and GeneticsAssam > Agricultural UniversityJorhat-785013Assam, Indiaweb: www.aau.ac.in; > <http://www.aaau.ac.in> Phone: +91-376-2310526; +91-376231133(R); > 9435350529(M)* > -------------------------------------------------------------------------------------------------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-genetics mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-genetics [[alternative HTML version deleted]] _______________________________________________ R-sig-genetics mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
