getPRR: This function calculates the Proportional Reporting Ratio...
In winnenbr/GEA: Generalized Enrichment Analysis

Description Usage Arguments Details Value Examples

View source: R/functions.R

This function will detect signals for given adverse drug event pair based on the biomedical literature (MEDLINE).

1	getPRR(atccode, event, abstraction = getAbstractionLayer(c(4, 7)))

`atccode`	The ATC code for the drug of interest.
`event`	The MeSH term for the adverse event of interest.
`abstraction`	The abstraction layer object for specified abstraction level.

Constructs a contingency table for given drug and adverse event based on theit occurrrences and co-occurrences in the literature set (provided by the abstraction layer object), aggregates terms to specified abstraction level. Performs zero-cell correction. Returns PRR for given drug - adverse event pair.

PRR for given drug - adverse event pair

{

  library("GEA")
  
  drugs <- Drugs("drugs_ATC_MEDLINE_360k.txt")
  events <- AdverseEvents("manifestations_MEDLINE_360k.txt")
  abs710    <- getAbstractionLayer(drugs,events,c(7,10))
  
  getPRR("R03DC01","D058186",abs710)
}