I am very new in haplotype analysis and have faced with some problems that I do not know how to solve.
I want to generate haplotype networks for sodium channel (DKr gene) in anopheles species. I have converted my vcf into fast file, produced multiple alignment with ClustalW and I am using “Pegas” package in R in order to generate the networks.
This is simply the R-code that I am using
library("ape") library("pegas") naso<-read.dna("test.2.fasta", format="fasta") naso # list of indivduals table(rownames(naso)) nasoHaps1 <- haplotype(naso) nasoHaps1 ind.hap<-with( stack(setNames(attr(nasoHaps1, "index"), rownames(nasoHaps1))), table(hap=ind, pop=rownames(naso)[values]) ) ind.hap[1:10, 1:9] #print just a chunk net <- haploNet(nasoHaps1) plot(net, size = attr(net, "freq")) plot(nasoNet, size=attr(net, "freq"), scale.ratio = 2, cex = 0.8, pie=ind.hap) legend(50,50, colnames(ind.hap), col=rainbow(ncol(ind.hap)), pch=20)
I keep getting these error message:
> Warning messages: 1: In haplotype.DNAbin(naso) : some sequences of > different lengths were assigned to the same haplotype 2: In > haplotype.DNAbin(naso) : some sequences were not assigned to the > same haplotype because of ambiguities
Could someone please guide me how I can resolve these two! how can I find ambiguous positions?
I appreciate any help.
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