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Query antimicrobial phenotype (AST) data from NCBI Pathogen Detection BigQuery

Source: R/query_ncbi_bq.R
query_ncbi_bq_ast.Rd

This function queries the ncbi-pathogen-detect.pdbrowser.ast BigQuery table to retrieve antimicrobial susceptibility testing (AST) data from NCBI Pathogen Detection.

Usage

query_ncbi_bq_ast(
  taxgroup,
  antibiotic = NULL,
  force_antibiotic = FALSE,
  project_id = NULL
)

Arguments

taxgroup

String specifying the organism group to filter on (e.g., "Pseudomonas aeruginosa"). See https://www.ncbi.nlm.nih.gov/pathogens/organisms/ for a list. Required.

antibiotic

(Optional) String (or vector of strings) specifying the antibiotic name/s to filter on (default NULL). Uses the AMR package to try to fix typos, and format to lower-case.

force_antibiotic

(Optional) Logical indicating whether to turn off parsing of antibiotic names and match exactly on the input strings (default FALSE).

project_id

(Optional) Google Cloud Project ID to use for billing. If NULL (default), looks for GOOGLE_CLOUD_PROJECT environment variable.

Value

A tibble containing AST data with columns renamed to match import_ncbi_ast() expectations.

Details

Requires Google Cloud authentication. Run bigrquery::bq_auth() before first use, or set up application default credentials via gcloud auth application-default login.

Examples

if (FALSE) { # \dontrun{
# Query AST data for Klebsiella pneumoniae, filtered to meropenem
ast_raw <- query_ncbi_bq_ast(
  taxgroup = "Klebsiella pneumoniae",
  antibiotic = "meropenem"
)

# Import and reinterpret using CLSI breakpoints
ast <- import_ncbi_ast(ast_raw, interpret_clsi = TRUE)
} # }