Nothing
get_kegg_groups=function(all_orgs){
groups=unique(unlist(strsplit(all_orgs$phylogeny, ";")))
}
is_group=function(group, all_orgs){
groups=get_kegg_groups(all_orgs)
if (!group%in%groups) return(FALSE)
return(TRUE)
}
is_organism=function(organism){
if (!organism%in%names(orgs_cpds)) return(FALSE)
return(TRUE)
}
get_organisms_in_group=function(group, all_orgs){
if (!is_group(group, all_orgs)) stop("Invalid group.")
group_search=paste(".*", group, ".*", sep="")
organisms=as.character(all_orgs$organismCode[grep(group_search, all_orgs$phylogeny)])
return(organisms)
}
compounds_in_organism=function(organism){
#if (!is_organism(organism)) stop("Invalid organism code.")
compounds=orgs_cpds[[organism]]
return(compounds)
}
compounds_in_group=function(group, all_orgs){
#Compound only needs to be in one of the organisms' group to be considered present.
organisms=get_organisms_in_group(group, all_orgs)
compounds_group=c()
for(organism in organisms){
compounds_organism=compounds_in_organism(organism)
compounds_group=unique(c(compounds_group, compounds_organism))
}
return(compounds_group)
}
is_compound_in_organism=function(compound, organism){
if (!is_organism(organism)) stop("Invalid organism code.")
if (compound %in% compounds_in_organism(organism)) return(TRUE)
return(FALSE)
}
is_compound_in_group=function(compound, group, all_orgs){
if (!is_group(group, all_orgs)) stop("Invalid group.")
if (compound %in% compounds_in_group(group, all_orgs)) return(TRUE)
return(FALSE)
}
is_compound_in_entity=function(compound, entity, all_orgs){
#entity: string of organism or group.
#If entity is a group:
if(is_group(entity, all_orgs)) return(is_compound_in_group(compound, entity, all_orgs))
if(is_organism(entity)) return(is_compound_in_organism(compound, entity))
stop("Invalid entity.")
}
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