data-raw/phecode_map.R

In vcastro/Phecode: Phecode definitions and mappings to ICD-9 and ICD-10 codes

library(tidyverse)
library(fuzzyjoin)
source('data-raw/utils.R')

download_extract(url = "https://phewascatalog.org/files/phecode_icd9_map_unrolled.csv.zip",
                 exdir = "data-raw",
                 files = c("phecode_icd9_map_unrolled.csv"))



Phecode_icd9_map <- read_csv("data-raw/phecode_icd9_map_unrolled.csv", 
                                col_types = cols(.default = col_character())) %>% 
  mutate(vocabulary_id = 'ICD9CM') %>% 
  select(code = icd9, phecode, vocabulary_id)


phecode_list <- Phecode_icd9_map %>% select(parent_phecode = phecode) %>% 
  #rbind(parent_phecode = "305") %>%   #missing this parent code in icd9
  unique()


Phecode_icd9_map_unrolled <- Phecode_icd9_map %>% 
  fuzzy_right_join(phecode_list, by = c("phecode" = "parent_phecode"), 
                   match_fun = like_match) %>% 
  select(code, phecode = parent_phecode, vocabulary_id) %>% 
  unique()


#### ICD-10-CM

download_extract(url = "https://phewascatalog.org/files/Phecode_map_v1_2_icd10cm_beta.csv.zip",
                 exdir = "data-raw",
                 files = c("Phecode_map_v1_2_icd10cm_beta.csv"))

Phecode_icd10cm_map <- read_csv("data-raw/Phecode_map_v1_2_icd10cm_beta.csv", 
                             col_types = cols(.default = col_character()), 
                             locale = readr::locale(encoding = "UTF-8")) %>% 
  mutate(vocabulary_id = 'ICD10CM')


phecode_list <- Phecode_icd10cm_map %>% select(parent_phecode = phecode) %>% unique()


Phecode_icd10cm_map_unrolled <- Phecode_icd10cm_map %>% 
  fuzzy_right_join(phecode_list, by = c("phecode" = "parent_phecode"), 
                   match_fun = like_match) %>% 
  select(code = icd10cm, phecode = parent_phecode, vocabulary_id) %>% 
  unique()


### ICD-10


download_extract(url = "https://phewascatalog.org/files/Phecode_map_v1_2_icd10_beta.csv.zip",
                 exdir = "data-raw",
                 files = c("Phecode_map_v1_2_icd10_beta.csv"))

Phecode_icd10_map <- read_csv("data-raw/Phecode_map_v1_2_icd10_beta.csv", 
                              col_types = cols(.default = col_character()), 
                              locale = readr::locale(encoding = "UTF-8")) %>% 
  mutate(vocabulary_id = 'ICD10')


phecode_list <- Phecode_icd10_map %>% select(parent_phecode = PHECODE) %>% unique()


Phecode_icd10_map_unrolled <- Phecode_icd10_map %>% 
  fuzzy_right_join(phecode_list, 
                   by = c("PHECODE" = "parent_phecode"), 
                   match_fun = like_match) %>% 
  select(code = ICD10, phecode = parent_phecode, vocabulary_id) %>% 
  unique()



### COMBINED MAP AVAILABLE ON PHEWAS_CATALOG

download_extract(url = "https://phewascatalog.org/files/ICD-CM_to_phecode_unrolled.txt.zip",
                 exdir = "data-raw",
                 files = c("ICD-CM to phecode, unrolled.txt"))

Phecode_icd9cm_icd10cm_map <- read_tsv("data-raw/ICD-CM to phecode, unrolled.txt", 
                              col_types = cols(.default = col_character()), 
                              locale = readr::locale(encoding = "UTF-8")) %>% 
                transmute(code = ICD,
                          phecode = phecode,
                          vocabulary_id = ifelse(flag == "9", "ICD9CM", "ICD10CM"))


### Put them all together

Phecode_map <- bind_rows(Phecode_icd9_map_unrolled, 
                         Phecode_icd10_map_unrolled,
                         Phecode_icd10cm_map_unrolled,
                         Phecode_icd9cm_icd10cm_map
                         ) %>% 
  filter(!is.na(vocabulary_id)) %>% 
  unique()


usethis::use_data(Phecode_map, overwrite = TRUE)