Renaming of drug_agent, antibiotic, etc.

[msberends]

From our feature ideas document:

Update colnames and parameter names to be clear when we are talking about an actual agent (phenotype) vs genes associated with agents or classes

Colnames:

• currently use 'drug_agent' in both geno and pheno tables, and binary matrix; and additionally 'drug_class' in geno tables as many markers are assigned to a class not a specific agent
• change to 'drug', 'drug_class'
• Parameters:
  • currently use antibiotic=xxx to select drugs in pheno tables, and drug_class_list=c(X,X) to select markers by class in geno tables
  • change to pheno_drug=xxx when filtering a pheno table based on the agent that was measured (recorded in 'agent' column in a pheno table)
  • geno_class=xxx or geno_drug=xxx when filtering a genotype table based on categories the gene has been annotated with / assigned to
  • Check for all remaining instances of ‘antibiotics’, ‘agent’