getDefaultConfig: Default configuration
In INRA/rgs3: R package wrapping the GS3 program for genomic selection

Description Usage Arguments Value Author(s) See Also

Return a list corresponding to a default configuration as used in the vignette.

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getDefaultConfig(data.file = NA, genos.file = NA, ped.file = "",
  nb.snps = NA, method = "VCE", ptl = NULL, twc = c(NA, 0),
  rec.id = NA, use.mix = "F", blasso = FALSE, task.id = "GS3")

`data.file`	path to the text file with the data (if not known yet, use NA instead of NULL)
`genos.file`	path to the text file with the genotypes (if not known yet, use NA instead of NULL)
`ped.file`	path to the text file with the pedigree (if not used, use NA or "" instead of NULL)
`nb.snps`	number of SNPs in the SNP genotype file
`method`	character with the method to use, among BLUP/MCMCBLUP/VCE/PREDICT
`ptl`	data frame indicating, for each effect, its position in the data file, its type, and its number of levels
`twc`	numeric vector containing the column index of the trait of interest in the data file, as well as the column index of its weights (0 if no weight)
`rec.id`	numeric corresponding to the column index of the genotype identifiers in the data file
`use.mix`	character indicating by `"T"` (or `"F"`) if the BayesCPi model should be fitted (or not)
`blasso`	logical indicating if the Bayesian Lasso model should be fitted (requires `method="VCE"` and `use.mix="F"`)
`task.id`	character containing the task identifier used as prefix for the output files