Description Usage Arguments Value Author(s) See Also
Perform K-fold cross-validation with GS3, and report metrics as advised in Daetwyler et al. (2013). Files are saved in the current directory.
1 2 3 | crossValWithGs3(genos, dat, config, task.id = "GS3", binary.trait = FALSE,
ped.file = "", afs = NULL, rep.id = 1, nb.folds = 10, seed = NULL,
remove.files = "some", nb.cores = 1, cl = NULL, verbose = 1)
|
genos |
matrix of SNP genotypes |
dat |
data frame with phenotypes |
config |
list containing the configuration for GS3 |
task.id |
character containing the task identifier used as prefix for the output files (for each fold, its index will be added) |
binary.trait |
logical |
ped.file |
path to the file containing the pedigree (if not used, use NA or "" instead of NULL) |
afs |
vector of allele frequencies which names are SNP identifiers (column names of |
rep.id |
identifier of the current replicate |
nb.folds |
number of folds |
seed |
if not NULL, this seed for the pseudo-random number generator will be used to shuffle genotypes before partitioning per fold |
remove.files |
remove files per fold (none/some/all); use |
nb.cores |
number of cores to launch folds in parallel (via |
cl |
object returned by |
verbose |
verbosity level (0/1/2); there will be a progress bar only for |
data frame
Helene Muranty, Timothee Flutre
crossValRepWithGs3
, getDefaultConfig
, writeConfigForGs3
, execGs3
, getPartitionGenos
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