yinlilin / kaml Goto Github PK

devtools::install_github("YinLiLin/R-KAML/KAML")

from URL https://api.github.com/repos/YinLiLin/R-KAML/zipball/master
Installation failed: Does not appear to be an R package (no DESCRIPTION)

Hello, is it possible to get some additional documentation? For example, I do not know what he, he-ai, brent models are. Same for MR, SR, BF. Also, are the defaults always the first possible argument? So MLM is the default model?

Cheers,
--Joseph

Hi, I couldn't generate the *.geno.desc file when I used your provided example data. I tried the hmp, vcf, plink and numeric data import the KAML.Data function, but showed the error as below:

Error in CreateFileBackedBigMatrix(as.character(backingfile), as.character(backingpath), :
Problem creating filebacked matrix.

MRO will not be supported from the next month. And already now I cannot download packages to an installation of MRO 4.0.2 I have on my PC. Have you maybe made a re-pack or know a walkaround to use? I would highly appreciate any advice.

Is there a straight-forward way to get a heritability estimation from KAML / quantify the variance explained by the predicted values?

Under windows the session is aborted and closed, impossible to execute

Possible problems with duparallel?

Warning for R version but call in your function , r.open <- !inherits(try(Revo.version, silent=TRUE),"try-error"). Revo.version only under 4.0.2 ...

_Microsoft R Open 4.0.2
The enhanced R distribution from Microsoft
Microsoft packages Copyright (C) 2020 Microsoft Corporation

Using the Intel MKL for parallel mathematical computing (using 4 cores)_

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

Hi YinLiLin

I wonder if I can fit the dominance matrix by using the kinship matrix by KAML() function? Can KAML make use of both gfile and kinship at the same time? If yes, is that way can calculate the dominance effect?

Thanks
Vu

请问尹博士，KAML有LD阈值设定的功能吗？我在说明书上没有找到

Hi,
First of all, thank you for developing the wonderful software. I used all my samples as training data to train a predictive model and the final output is listed below. I want to know the prediction accuracy of the model I got, which is a QTN+K model. It seems I can use Cross-validation to assess my model, but I didn't know how to do that. Is there a parameter in KAML to do that, or I need to do it by myself?

List of 12
 $ y       : num [1:376, 1] 27.9 29.6 29.7 28.5 29.6 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr "FL"
 $ beta    : num 29.3
 $ gebv    : num [1:376, 1] -1.478 0.248 0.318 -0.859 0.276 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr "FL"
 $ vg      : num [1, 1] 1.09
 $ ve      : num 1.07
 $ qtn     : num [1:2] 1909343 1234880
 $ qtn.eff : num [1:2] -0.383 -0.471
 $ model   : chr "QTN+K"
 $ weight  : num [1:2658921] 0.987 0.987 0.987 0.987 0.987 ...
 $ top.perc: num 0.000923
 $ logx    : num 1.11
 $ K       : num [1:376, 1:376] 0.8634 0.3642 0.0102 -0.0312 -0.1829 ...

Hi, hope you are doing well.
I am trying KAML for some data but I always get this error:
Cross-validation Finished_2.00%Error in mult.store[, 2] : subscript out of bounds

And this for a different data:
Pick up pseudo QTNs at LD threshold(0.3) as following:
Error in if (sum(p_cor > cor.threshold) == 0) bin.qtn[[g]] <- c(bin.qtn[[g]], :
missing value where TRUE/FALSE needed

Would you please help with these issues? Thanks!

Hi YiLiLin.

Sorry to bother you again.
I am tring to run binary (survival) trait code as 0, 1 and NA in KAML but can not finish the run. It run well with continuous trait. Please see the screenshot.

Do my phenotype data format is wrong?

I ran this:
iter1test1 <- KAML(pfile="pheno_iter1test1.txt", pheno=1, dcovfile="dcov_tracatfish.txt", qcovfile="qcov_tracatfish.txt", gfile="tracatfish", sample.num=20, crv.num=5)

Regards,

Vu

Firsly, if you run into some errors with types of non-zero exit status when you install devtools, it means some required packages are not installed in the system, which can be handled as follows:

sudo apt-get -y install libcurl4-gnutls-dev libxml2-dev libssl-dev

Secondly, if you run into github.api error, you can solve it by the following command:

devtools::install_github("YinLiLin/R-KAML", host = "https://api.github.com")

Thirdly, if you run into tar type of error, it may be because the defualt downloading tools was not libcurl but curl, which can be solved with the following command:

options("download.file.method" = "libcurl")

Best,
Zhe

hi, lilin

How can i calculate the accuracy of this model?