writeConfigForGs3: Write configuration

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

Description

Write the configuration file for GS3.

Usage

writeConfigForGs3(config, task.id = "GS3")

Arguments

config

list containing the configuration for GS3 via the following components: num.loci number of loci method BLUP/MCMCBLUP/VCE/PREDICT simul one-letter character indicating if simulations should be performed (T) or not (F) niter number of iterations for the Gibbs sampler burnin burn-in for the Gibbs sampler thin thinning for the Gibbs sampler conv.crit convergence criterion (meaningful if BLUP) correct correction (to avoid numerical problems) vcs.file path to the text file to which the variance component samples will be written sol.file path to the text file to which the solutions will be written twc 2-element vector which first element corresponds to the column index of the trait values in the data file, and the second to the column index of the weights in the data file (use 0 if no weight) num.eff number of effects ptl 3-column data frame indicating, for each covariable/factor, its position (column) in the data file, type of effect and number of levels vc 3-column data frame indicating, for each variance component, its expected value and degrees of freedom rec.id 1-element vector indicating the column in the data file corresponding to the genotype identifiers cont vector with T or F indicating if the MCMC run is a continuation of a previous, interrupted one mod vector with T or F for each covariable/factor indicating if it has to be included or not in the model ap prior proportions of the BayesCPi mixture dp prior proportions of the BayesCPi mixture use.mix one-letter character indicating if the Bayes C pi prior should be used (T) or not (F) blasso boolean indicating if the Bayesian lasso prior should be used or not

task.id

character containing the task identifier used as prefix for the configuration file; will be followed by "_config.txt"

Value

path to the text file to which the configuration for GS3 will be written

Author(s)

Timothee Flutre

See Also

getDefaultConfig, execGs3

INRA/rgs3 documentation built on May 20, 2019, 5:24 p.m.