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GS3 returned the following error:

At line 1199 of file gs3.f90 (unit = 10, file = 'config.txt')
Fortran runtime error: Bad integer for item 1 in list input

It seems to be due to the fact that NITER is written as 1e+05 instead of 100000.

To eventually prevent continuation of the MCMC when execGs3()is run several times in the same directory.

Dear Timothée,

I was trying to download rgs3 from github but it failed, so I cloned the git repo and tried to build it myself on debian, Unfortunaltely, I am having problems. Do you think you could help?
Best Gregor

R CMD build rgs3

• checking for file ‘rgs3/DESCRIPTION’ ... OK
• preparing ‘rgs3’:
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ... ERROR
  --- re-building ‘crossval-rgs3.Rmd’ using rmarkdown
  Quitting from lines 137-147 (crossval-rgs3.Rmd)
  Error: processing vignette 'crossval-rgs3.Rmd' failed with diagnostics:
  isValidData(dat, NULL, col.id, col.trait, binary.trait) ist nicht TRUE
  --- failed re-building ‘crossval-rgs3.Rmd’

--- re-building ‘intro-rgs3.Rmd’ using rmarkdown
Quitting from lines 308-311 (intro-rgs3.Rmd)
Error: processing vignette 'intro-rgs3.Rmd' failed with diagnostics:
isValidData(x, inds, col.id, col.traits, binary.traits) ist nicht TRUE
--- failed re-building ‘intro-rgs3.Rmd’

SUMMARY: processing the following files failed:
‘crossval-rgs3.Rmd’ ‘intro-rgs3.Rmd’

Fehler: Vignette re-building failed.
Ausführung angehalten

In writeDataForGs3, the default value for binary.traits as only one value, but if there are missing data, binary.traits is expected to be a vector of length the number of columns of x because there is a test on binary.traits[c] with c in 1:ncol(x).

However, at the beginning there is a test on length(binary.traits) == length(col.traits) so length(binary.traits) cannot be ncol(x)

I think replacing
if (binary.traits[c]) {
by
if (binary.traits[which(c == col.traits)]) {
should work.

Hélène

It's seems that the GS3 manual at http://genoweb.toulouse.inra.fr/~alegarra/gs3_folder/ is not up-to-date (May 2014). The github repository contains a more recent version (Nov. 2016).
The link in the rgs3 vignette should probably therefore be modified to:
https://github.com/alegarra/gs3/blob/master/manual/manualgs3_6.pdf
or
https://github.com/alegarra/gs3/raw/master/manual/manualgs3_6.pdf
for a direct download.

I found a problem in the way missing data are handled in writeDataForGs3: if the data.frame with the phenotypic data has several columns before the trait of interest and these columns contain missing data, for the moment writeDataForGs3 will not transform them into -9999 and this will prevent reading data further by gs3. I had a phenotypic dataset with a missing data in the second trait at the 6th line, and when I asked for analysis of the third trait, only 5 records were read.

Concerning writeGenosForGs3, as gs3 can work with missing data in the genotypic data, and these have to be coded as "5", writeGenosForGs3 should accept values of 5 in the matrix of genotypic data.
So the stopping rules at the beginning should be
stopifnot(is.matrix(x), all(x %in% c(0, 1, 2, 5)), !is.null(rownames(x)),
is.vector(inds), is.numeric(inds), !is.null(names(inds)),
all(inds == 1:length(inds)), all(rownames(x) %in% names(inds)))

Hope this helps !

Hélène

Seems to be due to the usage of invisible in function execGs3.

Currently, the output files of the i-th fold are sol.txt_foldi, config_train_gs3_foldi.txt_finalEstimates, ..., which can be overwritten if several jobs run in the same directory.

In some data sets, genotypes have been phenotyped several times, but some of these data could be missing, which currently results in a NA in cross-validation results such as the RMSPE.

This should be doable by executing GS3 without any configuration file, and parsing the stdout or stderr.

2varapqpi -> X2varapqpi

Look at this task view, and notably at the parallel and doParallel packages.

install and library loading is OK but I couldn't the vignette on Windows:

browseVignettes("rgs3")
No vignettes found by browseVignettes("rgs3")

The histogram of gEBVs in vignette "intro-gs3" is not centered on 0, why?