bioconductor-faers

name	bioconductor-faers
description	The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.

faers

Workflows

Standard Workflow

library(faers)

# 1. Check metadata of FAERS
faers_meta(internal = TRUE)

# 2. Download and parse quarterly data files
data2 <- faers(
  c(2004, 2017), 
  c("q1", "q2"), 
  dir = system.file("extdata", package = "faers"), 
  compress_dir = tempdir()
)

# 3. Retrieve specific field data (e.g., demographic data)
demo_data <- faers_get(data2, "demo")

# 4. Load standardized data and retrieve MedDRA hierarchy
data_std <- readRDS(system.file("extdata", "standardized_data.rds", package = "faers"))
meddra_hier <- faers_meddra(data_std, use = "hierarchy")

Input/Output Note: Inputs are year, quarter, and directory paths for FAERS raw data; outputs are standardized FAERS data tables and MedDRA hierarchy mappings.

When to Use

• Accessing and parsing the FDA Adverse Event Reporting System (FAERS) quarterly data files.
• Retrieving specific demographic, drug, or reaction fields using faers_get.
• Standardizing drug and reaction terms to MedDRA terminology using faers_standardize and faers_meddra.

When NOT to Use

• For analyzing clinical trial adverse events that are not part of the FAERS public database.
• For real-time adverse event tracking (FAERS data is released quarterly).

Data Requirements

• Raw FAERS quarterly data files (ASCII or XML format).
• MedDRA terminology files for standardization.

Key Parameters

• internal (FALSE): Logical indicating whether to use internal cached FAERS metadata in faers_meta.
• dir: Directory path where FAERS data files are stored or downloaded.
• compress_dir: Temporary directory for uncompressing downloaded files.
• use ("hierarchy"): Component of MedDRA to retrieve (e.g., "hierarchy" or "SMQ").

Best Practices

• Check FAERS metadata using faers_meta(internal = TRUE) to verify available quarters and file sizes before downloading.
• Use faers_combine to merge multiple quarters of parsed FAERS data into a single object.
• Standardize drug and reaction terms using faers_standardize with a valid MedDRA path to ensure consistent terminology.

Common Pitfalls

• Attempting to run standardization without providing a valid path to uncompressed MedDRA data. Ensure meddra_path is correctly specified.

Alternatives

• openfda: For querying the OpenFDA API directly instead of parsing raw quarterly files.

Citations

• FDA Adverse Event Reporting System (FAERS) documentation.

References

• Homepage: bioconductor.org/packages/faers
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/faers/inst/doc/FAERS-Pharmacovigilance.html