Difficulty with msaConvert function in R package
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@25b49ca9
Last seen 8 months ago
Portugal

Hello,

I have been using the "msa" R package, and it has been working great. However, I recently got some warning messages when using the "msaConvert" function to convert an "MsaDNAMultipleAlignment" object into a "DNAbin" object. The warning messages are as follows:

Code should be placed in three backticks as shown below

#Input
library(msa)
converted<- msaConvert(alignment,type="ape::DNAbin")

#output
Base composition:
a   c   g   t
NaN NaN NaN NaN
(Total: 5.82 kb)
Warning messages:
1: In f(x) : NAs introduced by coercion
2: In f(x) : NAs introduced by coercion
3: In f(x) : out-of-range values treated as 0 in coercion to raw


My alignment object seems to be fine, the trouble happens when converting into the "DNAbin".

The problem is further noticeable when I try to construct a distance matrix out of my alignment using the "ape" package using the following command:

matrix_dist<-dist.dna(converted, model = "K80",as.matrix = T)


Do you have any suggestions that may resolve the issue or any idea what may be causing it?

Thank you so much, João

ape msa • 370 views
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Entering edit mode
UBodenhofer ▴ 290
@ubodenhofer-5425
Last seen 14 days ago
University of Applied Sciences Upper Au…

Sorry for the late reply here, I overlooked this post. We have sorted this out already in a private communication. However, I want to share the reply with the community, even if it comes really late:

This issue is caused by a change in the interface of the 'ape' package. It should be fixed in the next release (current devel). There is also a workaround in case that you can't/don't want to wait:

### Do not load the ‘ape’ package yet!
alignment <- msa(mySequences, type="dna",method="ClustalW")
converted<- msaConvert(alignment, type="ape::DNAbin")
class(converted) <- "matrix"

## now load ‘ape’
library(ape)
converted <- as.DNAbin(converted)
## now ‘converted’ is a proper ‘DNAbin’ object

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