Compute marker effects per environment with Elastic Net — marker_effect_per_env

In each environment of the MET dataset, marker effects are computed separately.

marker_effect_per_env_EN(
  geno,
  pheno,
  environment,
  pheno_trait,
  nb_folds_cv = 4,
  reps = 2,
  ...
)

Arguments

geno	`data.frame` with markers in columns and inviduals in rows. Typical input is `METData$geno` from the `create_METData()` function.
pheno	`data.frame` with: First column: ID genotypes Second column: year Third column: location Subsequent columns: phenotypic traits with names indicated in colnames() Last column: IDenv (combination LocationxYear) Typical input is `METData$pheno` from the `create_METData()` function.
environment	`character` indicating the name of the environment for which marker effects should be computed
pheno_trait	`character` Name of the trait under study for which marker effects should be estimated
nb_folds_cv	`numeric` Number of folds in the CV process
reps	`numeric` Number of repeats of the k-folds CV

all_coef_avg data.frame

First column character contains the marker names.
Second column numeric the marker effects in this environment calculated by cross-validation with Elastic Net.
Third column character contains the environment name (combination LocationxYear).