frahik / bmtme Goto Github PK

I have SNP markers data of other species. I want to perform your model，but I found the genotypes of your rdata is not typical of 0,1,2

Is this package is able to install in Windows 10?
Because I am trying install and a failure occurs.

Thanks!

I would like to know if it is possible to use this package only with phenotypic data, without the constitution of the genetic relationship matrix, and if so, how?

Thank you in advance for your attention and availability.

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I can't find the ThreeWay data nor the fit function to perform the analysis here. I can find the data by following the publication link: http://hdl.handle.net/11529/10646

However, the fit function doesn't seem to work/exist. I can get the documentation to work, though...

the model predicted value, e.g. pm$results$Predicated
seems to leave out predicated values for one of folds in cross-validation.

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Researchgate include new citations:

https://www.researchgate.net/publication/331436792_An_R_Package_for_Bayesian_Analysis_of_Multi-environment_and_Multi-trait_Multi-environment_Data_for_Genome-Gased_Prediction

Hello,

Excited to try this new package on my multi-location, multi-year, and unbalanced data. However, I have run into the following error:

Error in matrix(nrow = nI, ncol = nI, 0L, dimnames = list(NULL, envNames)) : 
  length of 'dimnames' [2] not equal to array extent

My command:
fm.sm <- BMTME(Y = Ysm, X = Z.Esm, Z1 = Z.Gsm, Z2 = Z.EGsm, nIter = 10, burnIn = 2, thin = 1)

There is no issue up to this point. Obviously there is no error when I try the example commands in the manual.

Not sure where the error is coming from but my guess is that my unbalanced data is to blame. So my question is, how does BMTME handle missing trait values? If it is dropping genotypes with NA for trait value, then I can see the matrices being unequal.

Dimensions of all my input matrices are fine:

dim(Ysm)
1866    6
dim(Z.Esm)
1866   17
dim(Z.Gsm)
1866  396
dim(Z.EGsm)
1866 6732

Would appreciate your help & response. Thank you.