Get Genes Associated with a Phenotype

Returns the genes associated with a phenotype, given either its HPO identifier (e.g. "HP:0001250") or its name.

Usage

get_genes_for_phenotype(hpo_db, phenotype, exact = FALSE)

Arguments

hpo_db

An HPO dvobject returned by parseHPO.

phenotype

Character. An HPO identifier or a phenotype name.

exact

Logical. Used when phenotype is a name. If TRUE, the name must match exactly (ignoring case). If FALSE (default), any phenotype whose name contains phenotype matches.

Value

A tibble with columns gene_symbol, entrez_id, hpo_id, phenotype_name and association_weight, ordered by gene symbol.

See also

Other utility: add_database_info(), search_phenotypes(), show_dvobject_metadata(), subset_drugbank_dvobject(), subset_onsides_dvobject()

Examples

hpo_db <- parseHPO(system.file("extdata", "hpo_gene_attribute_edges.txt",
                               package = "dbparser"))
#> Parsing HPO gene-phenotype associations...
#> Parsed 7 genes, 352 phenotypes and 485 gene-phenotype associations.
get_genes_for_phenotype(hpo_db, "HP:0001250")
#> # A tibble: 3 × 5
#>   gene_symbol entrez_id hpo_id     phenotype_name association_weight
#>   <chr>       <chr>     <chr>      <chr>                       <dbl>
#> 1 KCNQ2       3785      HP:0001250 seizures                        1
#> 2 SCN1A       6323      HP:0001250 seizures                        1
#> 3 VDR         7421      HP:0001250 seizures                        1
get_genes_for_phenotype(hpo_db, "thrombosis")
#> # A tibble: 4 × 5
#>   gene_symbol entrez_id hpo_id     phenotype_name             association_weight
#>   <chr>       <chr>     <chr>      <chr>                                   <dbl>
#> 1 F2          2147      HP:0001977 abnormal thrombosis                         1
#> 2 F2          2147      HP:0002625 deep venous thrombosis                      1
#> 3 F2          2147      HP:0004936 venous thrombosis                           1
#> 4 F2          2147      HP:0005305 cerebral venous thrombosis                  1