Parse HPO Gene-Phenotype Associations

Reads the Human Phenotype Ontology (HPO) gene-phenotype associations as distributed by Harmonizome (gene_attribute_edges.txt) and returns a dvobject with gene, phenotype and association tables.

Usage

parseHPO(
  filepath,
  minimum_weight = 0,
  db_version = NULL,
  db_exported_date = NULL
)

Arguments

filepath

Character. Path to the Harmonizome HPO gene_attribute_edges.txt file, plain or gzip-compressed.

minimum_weight

Numeric. Minimum association weight to keep. The default 0 keeps all associations.

db_version

Character or NULL. Dataset version, stored in the object metadata.

db_exported_date

Character or NULL. Dataset release date, stored in the object metadata.

Value

A dvobject with three tibbles:

associations

One row per gene-phenotype pair: gene_symbol, entrez_id, hpo_id, phenotype_name and association_weight.

genes

Unique genes: gene_symbol, entrez_id and n_phenotypes, the number of associated phenotypes.

phenotypes

Unique phenotypes: hpo_id, phenotype_name and n_genes, the number of associated genes.

Details

The Harmonizome file is tab separated and has two header lines: the column names (source, source_desc, source_id, target, target_desc, target_id, weight) followed by a descriptor row (GeneSym, NA, GeneID, Phenotype, HPOID, NA, weight). The parser drops the descriptor row and renames the columns to domain-specific names. Columns that carry no information in this dataset (source_desc and the -666 placeholder in target_id) are not kept.

Gzip-compressed files (.gz) are read directly.

The resulting object can be linked to DrugBank target genes with merge_drugbank_hpo.

See also

Other parsers: cett_nodes_options(), drug_node_options(), parseDrugBank(), parseOnSIDES(), parseTWOSIDES(), references_node_options()

Examples

hpo_path <- system.file("extdata", "hpo_gene_attribute_edges.txt",
                        package = "dbparser")
hpo_db <- parseHPO(hpo_path)
#> Parsing HPO gene-phenotype associations...
#> Parsed 7 genes, 352 phenotypes and 485 gene-phenotype associations.
hpo_db$phenotypes
#> # A tibble: 352 × 3
#>    hpo_id     phenotype_name                          n_genes
#>    <chr>      <chr>                                     <int>
#>  1 HP:0000001 all                                           7
#>  2 HP:0000005 mode of inheritance                           7
#>  3 HP:0000118 phenotypic abnormality                        7
#>  4 HP:0000006 autosomal dominant inheritance                6
#>  5 HP:0000007 autosomal recessive inheritance               5
#>  6 HP:0000119 abnormality of the genitourinary system       4
#>  7 HP:0000152 abnormality of head or neck                   4
#>  8 HP:0000234 abnormality of the head                       4
#>  9 HP:0000707 abnormality of the nervous system             4
#> 10 HP:0000818 abnormality of the endocrine system           4
#> # ℹ 342 more rows
show_dvobject_metadata(hpo_db)
#> === BASIC INFO ===
#>      Class Total_DataFrames Top_Level_Lists Object_Size
#> 1 dvobject                3               0    132.9 Kb
#> 
#> === DATABASE METADATA ===
#>  Database Type Version Export_Date
#>  Original  HPO Unknown     Unknown
#> 
#> === DATA.FRAMES ===
#>          Path Rows Cols    Size
#>  associations  485    5 71.4 Kb
#>         genes    7    3    2 Kb
#>    phenotypes  352    3 58.3 Kb