Deleted:msa::dnds produces nan
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@22a915df
Last seen 7 weeks ago
Hong Kong

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Code should be placed in three backticks as shown below

b1 <- msa(a,type = "dna",method = "ClustalW")
b2 <- msa(a,type = "dna",method = "ClustalOmega")
b3 <- msa(a,type = "dna",method = "Muscle")

b3 <- msa::msaConvert(b3,type = "ape::DNAbin")
class(b3) <- "matrix"
converted <- as.DNAbin(b3)
a <- dnds(converted)
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Error in is(x, "MultipleAlignment") : object 'myAlignment' not found
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use default substitution matrix
using Gonnet
Warning in f(x) : NAs introduced by coercion
 7 %Warning in log(a) : NaNs produced
 9 %Warning in log(a) : NaNs produced
 11 %Warning in log(a) : NaNs produced
 13 %Warning in log(a) : NaNs produced
 15 %Warning in log(a) : NaNs produced
 16 %Warning in log(a) : NaNs produced
 18 %Warning in log(a) : NaNs produced
 25 %Warning in log(a) : NaNs produced
 29 %Warning in log(a) : NaNs produced
 31 %Warning in log(a) : NaNs produced
 33 %Warning in log(a) : NaNs produced
 100 %... done
dnds R msa • 64 views
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