"Population Differentiation for Sequence Data" Vignette

[mmlopezu]

@hlapp @zkamvar

I am having problems with the AMOVA analysis of sequence data.

FIRST APPROACH USING hierfstat:
Problem: when trying to convert a genind object to hierfstat, it gives me the following error:

"Error in genind2hierfstat(allData3) : 
  alleles must be encoded as integers or nucleotides. Exiting"

The object allData3 was a multidna object converted to genind and now I need to convert to hierfstat to run hierfstat

SECOND APPROACH USING pegas:
I am trying to run an AMOVA using the genetic distances calculated from a multidna object (allData2) and run into the following error:

allData_dist<-dist.multidna(allData2)
levels <- factor(c(rep("West", 20), rep("East", 20)))
populations <- factor(c(rep("CA", 10), rep("Ch", 10),rep("Am", 10), rep("AF", 10)))
amova(allData_dist ~ populations, nperm = 100)
"Error in y^2 : non-numeric argument to binary operator"

Any ideas how to solve any or both of these problems?

Thanks!
Margarita

[hlapp]

I am having problems with the AMOVA analysis of sequence data.

Which file are you referring to? PopDiffSequenceData.Rmd? Generally, it is always best to give the name of the file, that way it is unambiguous.

[hlapp]

And if the code you are having problems with is in a new file that's being developed by you, the first issue you are seeing we've also had in DifferentiationSNP.Rmd. The solution suggested there by @jgx65 actually worked; here's the code change: ee619ea.

[jgx65]

@mmlopezu @hlapp @zkamvar

re the conversion from genind to hierfstat, try this:

myData1<-read.FASTA("Ebom_CAD.fas") 

myData.genind<-DNAbin2genind(myData1,pop=rep(c("CA","Ch","Am","AF"), each=5)) 

myData.hierfstat<-genind2hierfstat(myData.genind)

wc(myData.hierfstat,diploid=FALSE)

Note the use of DNAbin2genind rather than as.genind.DNAbin on the second line.