pairnei-methods | R Documentation |
Function provides pairwise Nei's raw number of nucleotide differences between populations.
## 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)
x |
an object of class |
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 |
nperm |
the number of permutations. Set this to 0 to skip the permutation procedure. |
subset |
a vector of integers in the range [1, |
showprogbar |
boolean; whether the progress bar is displayed or not displayed. |
The null distribution of pairwise Nei's differences under the hypothesis of no difference between the populations is obtained by permuting individuals between populations.
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. |
signature(x = "Dna")
signature(x = "dist")
signature(x = "matrix")
Caner Aktas, caktas.aca@gmail.com
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.
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.