Can KAML run in the personal laptop/desktop?

[vunguyen1907]

Hi. I am trying to run KAML() but failed even in my laptop and desktop after all data were seemingly read correctly in to KAML. The error says. "R encountered a fatal error. The session was terminated". I did reinstall R and started over but the issue did not fix. Is it no enough RAM for the KAML to be run? Any suggestion? I have attached the screenshot.

Thanks

[YinLiLin]

There is a problem of compatibility between Rstudio and 'bigmemory' package, please try KAML in base R console.

[vunguyen1907]

Hi. I also tried in R console but it runs for 2 days with pending running so I force it to stop. But it works well by running in a server computer with 10 cores, 1TB ram.

I also have another question with the outputs. How can I check the genomic prediction accuracy value after 20 iterations/5 folds. I skim through str(mykaml) function object but hard to find.

Kind regards,

Vu

str(mykaml)
List of 8
$ y : num [1:560, 1] 32 10.2 18.8 28 67.4 ...
..- attr(, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr "tagweight"
$ beta : num 23.3
$ gebv : num [1:560, 1] 8.74 -13.06 -4.46 4.74 44.14 ...
..- attr(, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr "tagweight"
$ qtn : NULL
$ model : chr "K"
$ top.perc: num 0.0128
$ logx : num 9.32
$ K : num [1:560, 1:560] 0.92934 -0.01939 -0.0216 0.00834 0.08555 ...

[YinLiLin]

You need to implement a cross-validation to get the prediction accuracy for a trait, just set some of individuals as "NA", then run KAML to obtain the predicted gebv for those individuals, the prediction accuracy is the correlation between the original phenotype and the predicted gebv.

[vunguyen1907]

Hi YinLiLin. Thanks for your prompt response. Vu.