use duckdb to query NCBI Gene data in OSN bucket

Usage

remote_gene_query(
  gres = "gene2pubmed",
  qual = "limit 5",
  tname = basename(tempfile())
)

Arguments

gres: name of a gene resource, no suffix, see available_gene_parquet vector (unexported)
qual: a SQL fragment used to qualify a select * clause
tname: character(1) arbitrary name to use for internal sql table

Note

The httpfs extension for duckdb is installed when the function is called.

Examples

if (is_online()) {
remote_gene_query(qual = 'where "#tax_id" = 9606 limit 10;')
}
#> # A tibble: 10 × 3
#>    `#tax_id` GeneID PubMed_ID
#>        <dbl>  <dbl>     <dbl>
#>  1      9606      1   2591067
#>  2      9606      1   3458201
#>  3      9606      1   3610142
#>  4      9606      1   8889549
#>  5      9606      1  12477932
#>  6      9606      1  14702039
#>  7      9606      1  14760718
#>  8      9606      1  15221005
#>  9      9606      1  15461460
#> 10      9606      1  15489334