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Query antimicrobial genotype (MicroBIGG-E) data from NCBI Pathogen Detection BigQuery

Source: R/query_ncbi_bq.R
query_ncbi_bq_geno.Rd

This function queries the ncbi-pathogen-detect.pdbrowser.microbigge BigQuery table to retrieve genotype data. Note: This function only returns genotypes for BioSamples that also have AST data.

Usage

query_ncbi_bq_geno(
  taxgroup,
  geno_subclass = NULL,
  geno_class = NULL,
  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.

geno_subclass

(Optional) String or vector of strings specifying AMR subclasses to filter on (e.g., "CARBAPENEM").

geno_class

(Optional) String or vector of strings specifying AMR classes to filter on (e.g., "BETA-LACTAM"). Ignored if geno_subclass is specified.

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 genotype data with columns renamed to match import_amrfp() expectations.

Examples

if (FALSE) { # \dontrun{
# Query genotype data for Klebsiella pneumoniae samples that have AST data
geno_raw <- query_ncbi_bq_geno(
  taxgroup = "Klebsiella pneumoniae"
)

# Filter for carbapenem resistance genes and point mutations
geno_amrfp <- query_ncbi_bq_geno(
  taxgroup = "Klebsiella pneumoniae",
  geno_subclass = "CARBAPENEM"
)

geno <- import_amrfp(geno_amrfp, sample_col = "biosample_acc")
} # }