Turn a DGIdb genes response into a table

Pure. Rows come back in symbols order, one per input.

Usage

dgidb_parse_genes(body, symbols)

Arguments

body

A parsed DGIdb GraphQL response body.

symbols

The gene symbols that were queried, in the order asked.

Value

A tibble of symbol, concept_id, interaction_count, and source_url, one row per entry in symbols.

A real zero is not a miss

The distinction this parser exists to preserve. A gene DGIdb knows about with no recorded interactions has interaction_count = 0: that is an answer, and it means the gene is not currently druggable. A gene DGIdb has never heard of has interaction_count = NA: that is an absence of evidence.

Collapsing the two would tell a caller that an unknown gene is known not to be druggable, which is a different and much stronger claim than the data supports.

Examples

body <- list(data = list(genes = list(nodes = list(
  list(name = "NF1", conceptId = "hgnc:7765", interactions = list(list(), list()))
))))
dgidb_parse_genes(body, "NF1")
#> # A tibble: 1 × 4
#>   symbol concept_id interaction_count source_url                       
#>   <chr>  <chr>                  <int> <chr>                            
#> 1 NF1    hgnc:7765                  2 https://dgidb.org/genes/hgnc:7765