Severity/progression modifiers of each HPO term. In order of increasing severity:
HP:0012825 Mild (Severity_score=4)
HP:0012827 Borderline (Severity_score=3)
HP:0012828 Severe (Severity_score=2)
HP:0012829 Profound (Severity_score=1)
data("hpo_modifiers")data.table
annot <- HPOExplorer::load_phenotype_to_genes(3)
annot <- annot[modifier!=""]
parse_mod <- function(x){
unique(map_phenotypes(strsplit(x,";")[[1]]))
}
annot <- annot[,modifier_name:=lapply(modifier,parse_mod)][modifier!="",]
annot <- annot[,.(modifier_name=unlist(modifier_name)),
by=c("hpo_id","modifier","disease_name","aspect","disease_id")]
data.table::setnames(annot,"disease_id","disease_id")
dict <- HPOExplorer:::hpo_dict(type="severity")
annot$Severity_score <- dict[annot$modifier_name]
hpo_modifiers <- annot
usethis::use_data(hpo_modifiers, overwrite = TRUE)