In patelm9/chariot: chariot Package

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(chariot)
library(tidyverse)

conn <- connectAthena()

Pivoting the Concept Relationship table can provide a rich array representing the various relationships an OMOP Concept may have.

To exemplify, a test dataset of RxNorm and RxNorm Extension concepts are retrieved.

test_data <- 
  get_test_drug_concepts(conn = conn)

test_data

The relationships of these concepts are derived.

test_data_relationships <- lookup_relationships(test_data$concept_id,
                                                conn = conn)

test_data_relationships

To properly pivot the resultset, the concepts on both sides require transformation into a single cell per concept. This is achieved by converting concepts into the strip format.

test_data_relationships2 <-
  test_data_relationships %>%
  merge_strip(into = "concept_1", 
              suffix = "_1") %>%
  merge_strip(into = "concept_2",
              suffix = "_2")

test_data_relationships2

The dataset can now be pivoted by the relationship, hinging on concept_1, which are the concepts that were originally inputted.

output <-
  test_data_relationships2 %>%
  pivot_wider(id_cols = concept_1,
              names_from = relationship_id, 
              values_from = concept_2)
output

Since at times a concept_1 may have a specific relationship to more than 1 concept_2, a list-cols are returned in the output. To create a more readable output, an aggregate function on concept_2 must be supplied to convert multiple concept_2 values into a string of length 1.

output <-
  test_data_relationships2 %>%
  pivot_wider(id_cols = concept_1,
              names_from = relationship_id, 
              values_from = concept_2,
              # Add aggregate function
              values_fn = list(concept_2 = ~ paste(unique(.), collapse = "|"))
              )
output

The resulting dataset contains a row for each original concept provided with each relationship and concept/s it has the relationship to in a pipe-separated string.