R/check.mpp.cv.R

In mppR: Multi-Parent Population QTL Analysis

################
# check.mpp.cv #
################

# function to check the format of all elements introduced in the function
# mpp_CV


check.mpp.cv <- function(mppData, trait, Q.eff, VCOV, n.cores = 1, output.loc,
                         her){
  
  
  # 1. test the validity of the provided path to store the results
  
  if(!file.exists(output.loc)){
    
    stop("'output.loc' is not a valid path")
    
  }
  
  # 2. check mppData format
  
  check_mppData(mppData = mppData, Q.eff = Q.eff)
  
  # 3. check the trait
  
  check_trait(trait = trait, mppData = mppData)
  
  # 4. check Q.eff argument
  
  
  if (!(Q.eff %in% c("cr", "par", "anc", "biall"))){
    
    stop("'Q.eff' must be ", dQuote("cr"), ', ', dQuote("par"), ', ',
         dQuote("anc"), ' or ', dQuote("biall"))
    
  }
  
  # 5. check the VCOV argument
  
  
  if (!(VCOV %in% c("h.err", "h.err.as", "cr.err", "pedigree", "ped_cr.err"))){
    
    stop("'VCOV' must be ", dQuote("h.err"), ', ', dQuote("h.err.as"), ', ',
         dQuote("cr.err"), ', ', dQuote("pedigree"), ' or ',
         dQuote("ped_cr.err"))
    
  }
  
  # 6. test if the asreml function is present for the compuation of the
  # mixed models
  
  # if (VCOV != "h.err"){
  #   
  #   test <- requireNamespace(package = 'asreml', quietly = TRUE)
  #   
  #   if(!test){
  #     
  #     stop(paste("To use this type of VCOV, you must have access to the asreml",
  #                "function from the asreml-R package."))
  #     
  #   }
  #   
  #   message(paste("MESSAGE: Cross-validation",
  #                 "using mixed models is technically possible but can take",
  #                 "a hugh amount of time! Due to limited computer power, we",
  #                 "advice to only use the linear model (VCOV = 'h.err')."))
  #   
  #   text <- paste("Press [enter] to continue. If after you still want to stop",
  #                 "the process, Press Esc.")
  #   
  #   readline(prompt = text)
  #   
  # }
  
  # 7. Consistency for parallelization.
  
  
  if ((n.cores > 1) && (VCOV != "h.err")){
    
    stop("parallelization is only possible for 'VCOV' = ", dQuote("h.err")) 
      
    
  }
  
  
  # 8. check the format of her argument
  
  if((length(her) != 1) & (length(her) != mppData$n.cr)){
    
    stop("'her' must either be of length one representing the ",
         "average heritability over cross or a vector with one heritability ",
         "value per cross")
    
  }
  
  
}