R/checkInputs.R

In saezlab/PHONEMeS-ILP: Building logic-based models from discovery high-content phosphoproteomics data

#'\code{checkInputs}
#'
#'Checking inputs before Limma analysis
#'
#'Aurelien Dugourd
#'

checkInputs <- function(measurments, targets)
{
  if(class(measurments) != "data.frame")
  {
    error_message <- paste("The measurments argument should be a data.frame. It's currently a", paste(class(measurments), ".",sep = ""))
    return(list(FALSE, error_message))
  }
  else
  {
    if(dim(measurments)[1] == 0)
    {
      error_message <- "The measurments dataframe doesn't seem to contain any measurments..."
      return(list(FALSE, error_message))
    }
    else
    {
      if(dim(measurments)[2] == 0)
      {
        error_message <- "The measurments dataframe doesn't seem to contain any samples..."
        return(list(FALSE, error_message))
      }
      else
      {
        if(class(as.matrix(measurments)[,1]) != "numeric")
        {
          return(list(FALSE, "The measurments dataframe should contain only numerical values (or NAs)."))
        }
        else
        {
          if(class(targets) != "data.frame")
          {
            error_message <- paste("The targets argument should be a data.frame. It's currently a", paste(class(targets), ".",sep = ""))
            return(list(FALSE, error_message))
          }
          else
          {
            if(dim(targets)[2] < 2)
            {
              return(list(FALSE,"The targets dataframe should have at least two columns, sample names and conditions."))
            }
            else
            {
              if(dim(targets)[1] != dim(measurments)[2])
              {
                error_message <- paste("The targets dataframe should have as many samples (targets rows) as the measurements (measurments columns). Currently, the targets dataframe has", paste(dim(targets)[1], "samples and the measurements have", paste(dim(measurments)[2],"samples.")))
                return(list(FALSE, error_message))
              }
              else
              {
                
              }
            }
          }
        }
      }
    }
  }
  return(list(TRUE, "All seems to be in order..."))
}