# Provides the average number of pairwise Nei's (D) differences between populations Function provides pairwise Nei's raw number of nucleotide differences between populations. methods ```r ## S4 method for signature 'Dna' pairnei(x,populations,indels="sic",nperm=99, subset=NULL,showprogbar=FALSE) ## S4 method for signature 'dist' pairnei(x,populations,nperm=99, subset=NULL,showprogbar=FALSE) ## S4 method for signature 'matrix' pairnei(x,populations,nperm=99, subset=NULL,showprogbar=FALSE) ``` ## Arguments - `x`: an object of class `Dna`, `"dist"` or `"matrix"`. - `populations`: a vector giving the populations, with one element per individual. - `indels`: the indel coding method to be used. This must be one of "sic", "5th" or "missing". Any unambiguous substring can be given. See `distance` for details. - `nperm`: the number of permutations. Set this to 0 to skip the permutation procedure. - `subset`: a vector of integers in the range [1, `length(unique(populations))`], only distances between selected population(s) and the rest of the populations are calculated. If it is NULL, all comparisons are done. - `showprogbar`: boolean; whether the progress bar is displayed or not displayed. ## Details The null distribution of pairwise Nei's differences under the hypothesis of no difference between the populations is obtained by permuting individuals between populations. ## Returns a list with following components: - **`neidist`**: a matrix giving the average number of pairwise Nei's (D) differences between populations (below diagonal elements) and average number of pairwise differences within populations (diagonal elements). - **`p`**: a matrix giving the p-values, or NULL if permutation test is not performed. ## Methods - **`signature(x = "Dna")`**: - **`signature(x = "dist")`**: - **`signature(x = "matrix")`**: ## References Nei, M. and Li, W. H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. **Proceedings of the National Academy of Sciences of the United States of America** 76 , 5269-5273. ## Author(s) Caner Aktas, caktas.aca@gmail.com ## Examples ```r data("dna.obj") ### Method for signature 'Dna'. x<-dna.obj x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE] populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2", "pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4") ##skip permutation testing pn<-pairnei(x, populations, nperm=0) pn #Between populations as.dist(pn$neidist) #Within populations diag(pn$neidist) ##Gaps as missing characters. pn <-pairnei(x, populations, indels="m", nperm=0) pn ##using subset, third population against others pn<-pairnei(x, populations, nperm=0,subset=c(3)) pn ## Not run: ## 999 permutations. pn<-pairnei(x, populations, nperm=999, showprogbar=TRUE) pn ## random populations x<-dna.obj populations<-sample(1:4,nrow(x),replace=TRUE) pn<-pairnei(x, populations, nperm=999, showprogbar=TRUE) pn ## populations based on clusters x<-dna.obj d<-distance(x) hc<-hclust(d,method="ward.D") populations<-cutree(hc,4) pn<-pairnei(x, populations, nperm=999, showprogbar=TRUE) pn ## End(Not run) ### Method for signature 'dist'. x<-dna.obj x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE] populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2", "pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4") d<-distance(x) pn<-pairnei(d, populations,nperm=0) pn ### Method for signature 'matrix'. x<-dna.obj x<-dna.obj[c(1,20,21,26,27,28,30,3,4,7,13,14,15,16,23,24,25),,as.matrix=FALSE] populations<-c("pop1","pop1","pop1","pop1","pop1","pop1","pop1","pop2", "pop2","pop2","pop2","pop2","pop3","pop4","pop3","pop4","pop4") d<-as.matrix(distance(x)) pn<-pairnei(d, populations,nperm=0) pn ```

pairnei-methods function