config now includes data/geno/ped files; stat gen var comp now comput…

…ed in vcs2mcmc
INRA · Mar 4, 2018 · 4a33041 · 4a33041
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commit 4a33041
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Showing 11 changed files with 135 additions and 93 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rgs3
 Title: R package wrapping the GS3 program for genomic selection (http://
     snp.toulouse.inra.fr/~alegarra/)
-Version: 0.5.2
+Version: 0.5.3
 Authors@R: c(
     person("Timothée", "Flutre", email = "timothee.flutre@inra.fr", role = c("cre", "aut")),
     person("Hélène", "Muranty", email = "helene.muranty@inra.fr", role = c("ctb")))

diff --git a/R/gs3.R b/R/gs3.R
diff --git a/man/crossValFold.Rd b/man/crossValFold.Rd
diff --git a/man/crossValRepWithGs3.Rd b/man/crossValRepWithGs3.Rd
diff --git a/man/crossValWithGs3.Rd b/man/crossValWithGs3.Rd
diff --git a/man/getDefaultConfig.Rd b/man/getDefaultConfig.Rd
diff --git a/man/getPartitionGenos.Rd b/man/getPartitionGenos.Rd
diff --git a/man/vcs2mcmc.Rd b/man/vcs2mcmc.Rd
diff --git a/man/writeConfigForGs3.Rd b/man/writeConfigForGs3.Rd
diff --git a/vignettes/crossval-rgs3.Rmd b/vignettes/crossval-rgs3.Rmd
@@ -139,7 +139,6 @@ results.cv <- crossValWithGs3(
     dat = phenos,
     config = config,
     task.id = task.id,
-    ped.file = NULL,
     nb.folds = 5,
     seed = 123,
     remove.files = "all",

diff --git a/vignettes/intro-rgs3.Rmd b/vignettes/intro-rgs3.Rmd
@@ -334,12 +334,14 @@ Write the configuration file for GS3 (you can also use the helper function `getD
                    nlevels=c(Q,
                              0),
                    stringsAsFactors=FALSE))
-config <- list(num.loci=P,
+config <- list(data.file=phenos.file.gs3,
+               genos.file=genos.file.gs3,
+               ped.file="",
+               num.loci=P,
                method="VCE",
                simul="F",
-               niter=1*10^4,
-               burnin=1*10^3,
-               thin=10,
+               ## niter=2000, burnin=200, thin=2,     # debug
+               niter=1*10^4, burnin=1*10^3, thin=10,
                conv.crit="1d-8",
                correct=1000,
                vcs.file=paste0(getwd(), "/", task.id, "var.txt"),
@@ -360,9 +362,6 @@ config <- list(num.loci=P,
                blasso=FALSE)
 isValidConfig(config=config)
 config.file <- writeConfigForGs3(config=config,
-                                 data.file=phenos.file.gs3,
-                                 ped.file=NULL,
-                                 genos.file=genos.file.gs3,
                                  task.id=task.id)
 ```