Question: Haplotypic diversity with pegas package error
0
gravatar for mimi
12 months ago by
mimi20
mimi20 wrote:

Hello,

I'm trying to use haploNet function of {pegas} to plot a haplotype network, but i`m having an error. I can't build a haplotype net with the following script:

library(pegas)
S<- read.dna(file = "C:/Users/.....file.fasta", format ="fasta")
h<-haplotype(S)
net<-haploNet(h)
plot(h)

Error :

Error in integrate(L_jm, 0, 1, j = i, m = M) : non-finite function value
ADD COMMENTlink modified 12 months ago by zx87547.1k • written 12 months ago by mimi20

Did you manage to run it with example data provided with the package?

ADD REPLYlink written 12 months ago by zx87547.1k

Yes, I used it, but there is no fault. I would like to calculate the haplotypic diversity of 100 aligned bacterial genomes. (fasta file)

ADD REPLYlink written 12 months ago by mimi20
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