hpo_modifiers: Human Phenotype Ontology: disease modifiers

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

Human Phenotype Ontology: disease modifiers

Description

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)

Usage

data("hpo_modifiers")

Format

data.table

Source

Severity order

Column explanations

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)

neurogenomics/HPOExplorer documentation built on July 17, 2024, 3:12 p.m.