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genomics_ancest_disease_dispar/
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Ignored: data/icd/mondo_umls_mapping.csv
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | ba69411 | IJbeasley | 2025-12-29 | Fix some UMLS ICD10 Codes |
| html | 6bf9d47 | IJbeasley | 2025-12-29 | Build site. |
| Rmd | f597620 | IJbeasley | 2025-12-29 | Update mapping to ICD-10 codes (to keep year) |
| html | 1f555b6 | IJbeasley | 2025-12-29 | Build site. |
| Rmd | b4527b8 | IJbeasley | 2025-12-29 | Update mapping to ICD-10 codes |
| html | 757b4b4 | IJbeasley | 2025-10-09 | Build site. |
| Rmd | 6019c96 | IJbeasley | 2025-10-09 | Even more correcting of icd 10 codes |
| html | 0feea16 | IJbeasley | 2025-10-08 | Build site. |
| Rmd | a8f1628 | IJbeasley | 2025-10-08 | Include study accession in icd 10 map |
| html | 50ebebc | IJbeasley | 2025-10-08 | Build site. |
| Rmd | 9bbe0dd | IJbeasley | 2025-10-08 | Updating icd 10 mapping |
| html | ec027a3 | IJbeasley | 2025-10-08 | Build site. |
| Rmd | cb8a570 | IJbeasley | 2025-10-08 | Updating disease icd code mapping |
| html | 41d6fe5 | IJbeasley | 2025-09-28 | Build site. |
| Rmd | 97d340d | IJbeasley | 2025-09-28 | workflowr::wflow_publish("analysis/map_trait_to_icd10.Rmd") |
title: “Mapping GWAS traits to ICD 10” author: “Isobel Beasley” date: “2025-09-26” output: html_document —
library(dplyr)
library(stringr)
library(data.table)source(here::here("code/get_term_descendants.R"))# gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_group_v2.csv"))
gwas_study_info <- data.table::fread(here::here("output/gwas_cat/gwas_study_all_group.csv"))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms = stringi::stri_trans_general(collected_all_disease_terms, "Latin-ASCII")
)
# study accession = GCST003209
# replace benign neoplasm with colorectal cancer, endometrial cancer
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms = ifelse(STUDY_ACCESSION == "GCST003209" |
STUDY_ACCESSION == "GCST003208" ,
"colorectal cancer, endometrial cancer",
collected_all_disease_terms))
# for study accession = GCST90133383
# replace benign neoplasm with testicular cancer, hearing lossdisease_mapping <- gwas_study_info |>
filter(DISEASE_STUDY == T) |>
tidyr::separate_longer_delim(cols = collected_all_disease_terms,
delim = ", ") |>
select(`DISEASE/TRAIT`,
collected_all_disease_terms,
PUBMED_ID,
YEAR,
STUDY_ACCESSION) |>
distinct()
disease_mapping =
disease_mapping |>
filter(collected_all_disease_terms != "")
print("Number of unique disease trait & study pairs")[1] "Number of unique disease trait & study pairs"nrow(disease_mapping)[1] 46316diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms[gwas_study_info$collected_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
diseases <- unique(diseases)
print("Number of unique disease terms")[1] "Number of unique disease terms"print(length(diseases))[1] 1993DISEASE/TRAIT termsDISEASE/TRAIT Column to better match terms# removing genotype effect (e.g. (fetal genotype effect))
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` =
str_remove_all(`DISEASE/TRAIT`,
"\\s*\\([^)]*genotype effect\\)")
) |>
mutate(`DISEASE/TRAIT` =
str_remove_all(`DISEASE/TRAIT`,
"\\s*\\([^)]* effect\\)")
)
# remove '(adjusted for APOE e4 dosage)'
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\(adjusted for APOE e4 dosage\\)"))
# remove '(maternal):' & '(paternal):
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`, "\\s*\\(maternal\\):")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`, "\\s*\\(paternal\\):"))
# remove 'Biological Grandparent '
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`, "Biological Grandparent "))
# remove 'Biological Father: ', 'Biological Sibling: ', 'Biological Mother: '
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`, "Biological Father: ")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`, "Biological Sibling: ")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`, "Biological Mother: "))# remove (apnea hypopnea index),
# (average respiratory event duration),
# (micro-arousal index)
# (percentage of N3 sleep time during total sleep time)
# (percentage of N3 sleep time during sleep period time)
# (average oxyhemoglobin desaturation per event)
# (average oxyhemoglobin saturation across sleep episode)
# (percentage sleep with oxyhemoglobin saturation less than 90%)
# (wake time during sleep period time)
# (minimum oxyhemoglobin saturation across sleep episode)
# (oxygen desaturation index)
# (average oxygen saturation during sleep)
# (apnea hypopnea index, change over time)
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(apnea hypopnea index\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(average respiratory event duration\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(micro-arousal index\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(percentage of N3 sleep time during total sleep time\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(percentage of N3 sleep time during sleep period time\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(average oxyhemoglobin desaturation per event\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(average oxyhemoglobin saturation across sleep episode\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(percentage sleep with oxyhemoglobin saturation less than 90%\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(wake time during sleep period time\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(minimum oxyhemoglobin saturation across sleep episode\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(oxygen desaturation index\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(average oxygen saturation during sleep\\)")) |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(apnea hypopnea index, change over time\\)"))
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
" during REM sleep$| during non-REM sleep$"))
# ends in levels in coronary artery disease, make it just coronary artery disease
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` =
ifelse(str_detect(`DISEASE/TRAIT`,
"(?i)\\s*levels in coronary artery disease$"),
"coronary artery disease",
`DISEASE/TRAIT`))
# ends in levels in chronic kidney disease, make it just chronic kidney disease
# ends in levels in coronary artery disease, make it just coronary artery disease
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` =
ifelse(str_detect(`DISEASE/TRAIT`,
"(?i)\\s*levels in chronic kidney disease$"),
"chronic kidney disease",
`DISEASE/TRAIT`))
# ends in levels in type 2 diabetes, make it just type 2 diabetes
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` =
ifelse(str_detect(`DISEASE/TRAIT`,
"(?i)\\s*levels in type 2 diabetes$"),
"type 2 diabetes",
`DISEASE/TRAIT`))
# ends in levels in prediabetes, make it just prediabetes
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` =
ifelse(str_detect(`DISEASE/TRAIT`,
"(?i)\\s*levels in prediabetes$"),
"prediabetes",
`DISEASE/TRAIT`))
# remove str_extract(x, "(?<=Takes medication for )\\w+")
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` =
ifelse(str_detect(`DISEASE/TRAIT`,
"(?i)Takes medication for \\w+"),
str_extract(`DISEASE/TRAIT`,
"(?<=Takes medication for )\\w+"),
`DISEASE/TRAIT`))
# remove BMI adjustments
# '(BMI adjusted)', or '(adjusted for BMI)'
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(BMI adjusted\\)|\\s*\\(adjusted for BMI\\)"))
# remove 'trait'
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*trait$"))
# remove (slight), (severe), (generalised), (localised)
disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_remove_all(`DISEASE/TRAIT`,
"\\s*\\(slight\\)|\\s*\\(severe\\)|\\s*\\(generalised\\)|\\s*\\(localised\\)"))disease_mapping =
disease_mapping |>
mutate(`DISEASE/TRAIT` = str_squish(`DISEASE/TRAIT`))matched_icd10_desc =
phecodes |>
mutate(collected_all_disease_terms = tolower(iconv(ICD_DESCRIPTION,
to = "UTF-8"))
) |>
select(collected_all_disease_terms,
icd10_code = ICD10)
# filter missing strings
matched_icd10_desc =
matched_icd10_desc |>
filter(!is.na(collected_all_disease_terms) &
collected_all_disease_terms != "") |>
filter(!is.na(icd10_code) &
icd10_code != "")
matched_icd10_desc =
matched_icd10_desc |>
group_by(collected_all_disease_terms) |>
summarise(icd10_code = str_flatten(unique(icd10_code),
collapse = ", ",
na.rm = T),
.groups = "drop")
matched_icd10_desc =
matched_icd10_desc |>
mutate(icd10_code_origin = "ICD Description Match (DISEASE/TRAIT)")
# match by DISEASE/TRAIT
matched_icd10_desc =
matched_icd10_desc |>
rename(`DISEASE/TRAIT` = collected_all_disease_terms)
disease_mapping =
disease_mapping |>
rows_patch(matched_icd10_desc,
unmatched = "ignore")
print("Number of ICD10 codes obtained")[1] "Number of ICD10 codes obtained"disease_mapping |>
filter(!is.na(icd10_code)) |>
group_by(icd10_code_origin) |>
summarise(n = n(),
percent = n()/n_studies *100)# A tibble: 4 × 3
icd10_code_origin n percent
<chr> <int> <dbl>
1 ICD Description Match (DISEASE/TRAIT) 3945 8.52
2 Study PheCode (Manual Mapping) 875 1.89
3 Study PheCode Mapping 6780 14.6
4 Study Provided 3961 8.55phenotype_icd_map =
phecodes |>
group_by(Phenotype) |>
summarise(icd10_code =
str_flatten(ICD10,
collapse = ", ",
na.rm = T),
.groups = "drop")
matched_phenotypes =
phenotype_icd_map #|>
#filter(tolower(Phenotype) %in% not_found_diseases)
matched_phenotypes =
matched_phenotypes |>
mutate(collected_all_disease_terms = tolower(Phenotype)) |>
select(collected_all_disease_terms, icd10_code) |>
mutate(icd10_code_origin = "Phecode Phenotype Match (DISEASE/TRAIT)")
# match by DISEASE/TRAIT
matched_phenotypes =
matched_phenotypes |>
rename(`DISEASE/TRAIT` = collected_all_disease_terms)
disease_mapping =
disease_mapping |>
rows_patch(matched_phenotypes,
unmatched = "ignore")
disease_mapping |>
filter(icd10_code_origin == "Phecode Phenotype Match (DISEASE/TRAIT)") |>
nrow()[1] 580disease_mapping |>
filter(!is.na(icd10_code)) |>
group_by(icd10_code_origin) |>
summarise(n = n(),
percent = n()/n_studies *100)# A tibble: 5 × 3
icd10_code_origin n percent
<chr> <int> <dbl>
1 ICD Description Match (DISEASE/TRAIT) 3945 8.52
2 Phecode Phenotype Match (DISEASE/TRAIT) 580 1.25
3 Study PheCode (Manual Mapping) 875 1.89
4 Study PheCode Mapping 6780 14.6
5 Study Provided 3961 8.55matched =
disease_mapping |>
filter(icd10_code != "") |>
pull(collected_all_disease_terms)
not_found_diseases <- diseases[!diseases %in%
matched
]
not_found_diseases <- not_found_diseases[not_found_diseases != ""]
print(length(not_found_diseases))[1] 652unmapped_disease_terms <-
disease_mapping |>
filter(is.na(icd10_code)) |>
pull(`DISEASE/TRAIT`) |>
unique() |>
tolower()
# get UMLS CUIs with ICD10 mappings
umls_data <-
data.table::fread(here::here("data/icd/2025AA/META/MRCONSO.RRF"),
sep = "|",
header = FALSE,
quote = "",
fill = TRUE,
na.strings = c("", "NA")
)
colnames(umls_data)[1:18] <- c(
"CUI","LAT","TS","LUI","STT","SUI","ISPREF",
"AUI","SAUI","SCUI","SDUI","SAB","TTY","CODE",
"STR","SRL","SUPPRESS","CVF"
)
umls_cuis_icd10 <-
umls_data |>
filter(SAB %in% c("ICD10", "ICD10CM")) |>
select(CODE, CUI) |>
group_by(CUI) |>
summarise(CODE = str_flatten(unique(CODE),
collapse = ", ",
na.rm = T),
.groups = "drop"
) |>
rename(icd10_code = CODE)
umls_icd10 <-
umls_data |>
filter(CUI %in% umls_cuis_icd10$CUI)
umls_icd10 =
umls_icd10 |>
left_join(umls_cuis_icd10,
by = "CUI")
# overlap with umls terms
disease_trait_umls <-
umls_icd10 |>
filter(tolower(STR) %in% unmapped_disease_terms) |>
mutate(`DISEASE/TRAIT` = tolower(STR)) |>
# mutate(CODE = ifelse(SAB %in% c("ICD10", "ICD10CM"),
# CODE,
# NA)) |>
select(`DISEASE/TRAIT`,
icd10_code) |>
group_by(`DISEASE/TRAIT`) |>
summarise(icd10_code = str_flatten(unique(icd10_code),
collapse = ", ",
na.rm = T),
.groups = "drop"
) |>
distinct() |>
mutate(icd10_code_origin = "UMLS term match")
disease_mapping <-
disease_mapping |>
mutate(`DISEASE/TRAIT` = tolower(`DISEASE/TRAIT`)) |>
rows_patch(disease_trait_umls,
by = "DISEASE/TRAIT")collected_all_disease_terms
termsmatched_icd10_desc =
matched_icd10_desc |>
rename(collected_all_disease_terms = `DISEASE/TRAIT`)
matched_icd10_desc =
matched_icd10_desc |>
mutate(icd10_code_origin = "ICD Description Match (collected_all_disease_terms)")
disease_mapping =
rows_patch(disease_mapping,
matched_icd10_desc,
unmatched = "ignore")Matching, by = "collected_all_disease_terms"print("Number of ICD10 codes obtained")[1] "Number of ICD10 codes obtained"disease_mapping |>
filter(!is.na(icd10_code)) |>
group_by(icd10_code_origin) |>
summarise(n = n(),
percent = n()/n_studies *100)# A tibble: 7 × 3
icd10_code_origin n percent
<chr> <int> <dbl>
1 ICD Description Match (DISEASE/TRAIT) 3945 8.52
2 ICD Description Match (collected_all_disease_terms) 9575 20.7
3 Phecode Phenotype Match (DISEASE/TRAIT) 580 1.25
4 Study PheCode (Manual Mapping) 875 1.89
5 Study PheCode Mapping 6780 14.6
6 Study Provided 3961 8.55
7 UMLS term match 4820 10.4 matched =
disease_mapping |>
filter(icd10_code != "") |>
pull(collected_all_disease_terms)
not_found_diseases <- diseases[!diseases %in%
matched
]
not_found_diseases <- not_found_diseases[not_found_diseases != ""]
print(length(not_found_diseases))[1] 455matched_phenotypes =
matched_phenotypes |>
rename(collected_all_disease_terms = `DISEASE/TRAIT`)
matched_phenotypes =
matched_phenotypes |>
mutate(icd10_code_origin = "Phecode Phenotype Match (collected_all_disease_terms)")
# match by collected_all_disease_terms
disease_mapping =
disease_mapping |>
rows_patch(matched_phenotypes,
unmatched = "ignore")Matching, by = "collected_all_disease_terms"print("Number of ICD10 codes obtained")[1] "Number of ICD10 codes obtained"disease_mapping |>
filter(!is.na(icd10_code)) |>
group_by(icd10_code_origin) |>
summarise(n = n(),
percent = n()/n_studies *100)# A tibble: 8 × 3
icd10_code_origin n percent
<chr> <int> <dbl>
1 ICD Description Match (DISEASE/TRAIT) 3945 8.52
2 ICD Description Match (collected_all_disease_terms) 9575 20.7
3 Phecode Phenotype Match (DISEASE/TRAIT) 580 1.25
4 Phecode Phenotype Match (collected_all_disease_terms) 2194 4.74
5 Study PheCode (Manual Mapping) 875 1.89
6 Study PheCode Mapping 6780 14.6
7 Study Provided 3961 8.55
8 UMLS term match 4820 10.4 matched =
disease_mapping |>
filter(icd10_code != "") |>
pull(collected_all_disease_terms)
not_found_diseases <- diseases[!diseases %in%
matched
]
not_found_diseases <- not_found_diseases[not_found_diseases != ""]
print(length(not_found_diseases))[1] 442unmapped_terms <-
disease_mapping |>
filter(is.na(icd10_code)) |>
pull(collected_all_disease_terms) |>
unique()
# overlap with umls terms
collected_trait_umls <-
umls_icd10 |>
filter(tolower(STR) %in% unmapped_terms) |>
mutate(collected_all_disease_terms = tolower(STR)) |>
# mutate(CODE = ifelse(SAB %in% c("ICD10", "ICD10CM"),
# CODE,
# NA)) |>
select(collected_all_disease_terms,
icd10_code) |>
group_by(collected_all_disease_terms) |>
summarise(icd10_code = str_flatten(unique(icd10_code),
collapse = ", ",
na.rm = T),
.groups = "drop"
) |>
distinct() |>
mutate(icd10_code_origin = "UMLS term match (collected_all_disease_terms)")
disease_mapping <-
disease_mapping |>
rows_patch(collected_trait_umls,
by = "collected_all_disease_terms")manual_icd10_map <-
readxl::read_xlsx(here::here("data/icd/manual_disease_icd10_mappings.xlsx"))
manual_icd10_map =
manual_icd10_map |>
select(collected_all_disease_terms = mapped_trait,
icd10_code) |>
mutate(collected_all_disease_terms = stringr::str_squish(tolower(collected_all_disease_terms))) |>
mutate(icd10_code_origin = "Manual Mapping (collected_all_disease_terms)")
# disease_mapping =
# bind_rows(disease_mapping, to_add) |>
# distinct()
disease_mapping =
rows_patch(disease_mapping,
manual_icd10_map,
unmatched = "ignore")Matching, by = "collected_all_disease_terms"disease_mapping |>
filter(icd10_code_origin == "Manual Mapping (collected_all_disease_terms)") |>
nrow()[1] 1172# repeat for `DISEASE/TRAIT`
manual_icd10_map =
manual_icd10_map |>
select(`DISEASE/TRAIT` = collected_all_disease_terms,
icd10_code) |>
mutate(icd10_code_origin = "Manual Mapping (DISEASE/TRAIT)")
disease_mapping =
rows_patch(disease_mapping |> mutate(`DISEASE/TRAIT` = tolower(`DISEASE/TRAIT`)),
manual_icd10_map,
unmatched = "ignore")Matching, by = "DISEASE/TRAIT"disease_mapping =
disease_mapping |>
mutate(icd10_code = ifelse(collected_all_disease_terms == "toxicity" &
grepl("Anthracycline-induced cardiotoxicity|Trastuzumab-induced cardiotoxicity", `DISEASE/TRAIT`, ignore.case = T),
"I42.7, T45.1",
icd10_code)) |>
mutate(icd10_code_origin =
ifelse(collected_all_disease_terms == "toxicity" &
grepl("Anthracycline-induced cardiotoxicity|Trastuzumab-induced cardiotoxicity", `DISEASE/TRAIT`, ignore.case = T),
"Manual Mapping (from DISEASE/TRAIT)",
icd10_code_origin)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = ifelse(collected_all_disease_terms == "toxicity" &
grepl("Induration at the injection site after COVID-19", `DISEASE/TRAIT`, ignore.case = T),
"R23.4",
icd10_code)) |>
mutate(collected_all_disease_terms =
ifelse(collected_all_disease_terms == "toxicity" &
grepl("Induration at the injection site after COVID-19", `DISEASE/TRAIT`, ignore.case = T),
"induration of skin",
collected_all_disease_terms)) |>
mutate(icd10_code_origin =
ifelse(collected_all_disease_terms == "induration of skin",
"Manual Mapping (from DISEASE/TRAIT)",
icd10_code_origin)
)
# N64.5
disease_mapping =
disease_mapping |>
mutate(icd10_code = ifelse(collected_all_disease_terms == "toxicity" &
grepl("Induration \\(>= grade 2\\) in breast cancer treated with radiotherapy",
`DISEASE/TRAIT`, ignore.case = T),
"N64.5",
icd10_code)) |>
mutate(collected_all_disease_terms =
ifelse(collected_all_disease_terms == "toxicity" &
grepl("Induration \\(>= grade 2\\) in breast cancer treated with radiotherapy",
`DISEASE/TRAIT`, ignore.case = T),
"induration of breast",
collected_all_disease_terms)) |>
mutate(icd10_code_origin =
ifelse(collected_all_disease_terms == "induration of breast",
"Manual Mapping (from DISEASE/TRAIT)",
icd10_code_origin)
)
# T45.1
disease_mapping =
disease_mapping |>
mutate(icd10_code = ifelse(collected_all_disease_terms == "toxicity" &
grepl("Nivolumab-induced immune-related adverse events in cancer|Response to immune checkpoint inhibitors in melanoma",
`DISEASE/TRAIT`, ignore.case = T),
"T45.1",
icd10_code)) |>
mutate(icd10_code_origin =
ifelse(collected_all_disease_terms == "toxicity" &
grepl("Nivolumab-induced immune-related adverse events in cancer|Response to immune checkpoint inhibitors in melanoma",
`DISEASE/TRAIT`, ignore.case = T),
"Manual Mapping (from DISEASE/TRAIT)",
icd10_code_origin)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = ifelse(collected_all_disease_terms == "toxicity" &
grepl("Methotrexate-related central neurotoxicity in children treated for acute lymphoblastic leukemia",
`DISEASE/TRAIT`, ignore.case = T),
"G92, T45.1",
icd10_code)) |>
mutate(icd10_code_origin =
ifelse(collected_all_disease_terms == "toxicity" &
grepl("Methotrexate-related central neurotoxicity in children treated for acute lymphoblastic leukemia",
`DISEASE/TRAIT`, ignore.case = T),
"Manual Mapping (from DISEASE/TRAIT)",
icd10_code_origin)
)
## if DISEASE/TRAIT == Abnormalities of forces of labour
## and collected_all_disease_terms == abnormal delivery
## if icd10_code is missing, map to
disease_mapping =
disease_mapping |>
mutate(icd10_code = ifelse(collected_all_disease_terms == "abnormal delivery" &
grepl("^Abnormalities of forces of labour$",
`DISEASE/TRAIT`,
ignore.case = T) &
icd10_code == "",
"O62",
icd10_code)) |>
mutate(icd10_code_origin =
ifelse(collected_all_disease_terms == "abnormal delivery" &
grepl("^Abnormalities of forces of labour$",
`DISEASE/TRAIT`,
ignore.case = T),
"Manual Mapping (from DISEASE/TRAIT)",
icd10_code_origin)
)
## if DISEASE/TRAIT == Ischemic heart disease
## and collected_all_disease_terms == heart disease
## if icd10_code is missing, map to "I20-I21.6, I21.9-I25.9, Z82.4-Z82.49"
disease_mapping =
disease_mapping |>
mutate(icd10_code = ifelse(collected_all_disease_terms == "heart disease" &
grepl("^Ischemic heart disease$",
`DISEASE/TRAIT`,
ignore.case = T) &
icd10_code == "",
"I20-I21.6, I21.9-I25.9, Z82.4-Z82.49",
icd10_code)) |>
mutate(icd10_code_origin =
ifelse(collected_all_disease_terms == "heart disease" &
grepl("^Ischemic heart disease$",
`DISEASE/TRAIT`,
ignore.case = T),
"Manual Mapping (from DISEASE/TRAIT)",
icd10_code_origin)
)
# if collected_all_disease_terms == "heart disease"
# and icd10_code is missing
disease_mapping =
disease_mapping |>
mutate(icd10_code = ifelse(collected_all_disease_terms == "heart disease" &
icd10_code == "",
"C34",
icd10_code)) |>
mutate(icd10_code_origin =
ifelse(collected_all_disease_terms == "heart disease" &
icd10_code == "C34",
"Manual Mapping (collected_all_disease_terms)",
icd10_code_origin)
)# disease_mapping =
# disease_mapping |>
# filter(icd10_code != "")
matched <- c(disease_mapping_matched$collected_all_disease_terms,
matched_phenotypes$collected_all_disease_terms,
to_add$collected_all_disease_terms,
manual_icd10_map$collected_all_disease_terms)Warning: Unknown or uninitialised column: `collected_all_disease_terms`.
Unknown or uninitialised column: `collected_all_disease_terms`.not_found_diseases <- diseases[!diseases %in% matched]
not_found_diseases <- not_found_diseases[not_found_diseases != ""]
print(length(not_found_diseases))[1] 617# similar studies:
study_icd_map =
disease_mapping |>
filter(!is.na(icd10_code)) |>
filter(icd10_code_origin == "Study Provided" | icd10_code_origin == "Study PheCode Mapping")
study_icd_map =
study_icd_map |>
select(collected_all_disease_terms, icd10_code) |>
distinct()
# remove Z95.1 and Z95.5 from coronary artery disease
study_icd_map =
study_icd_map |>
mutate(icd10_code = ifelse(collected_all_disease_terms == "coronary artery disease",
str_replace_all(icd10_code, "Z95.1|Z95.5", ""),
icd10_code))
# assume ovarian cancer terms more specific than
# Malignant neoplasm of ovary and other uterine adnexa (PheCode 184.1)
# study_icd_map =
# study_icd_map |>
# filter(!( collected_all_disease_terms == "ovarian cancer" &&phecode == "184.10")
# )
study_icd_map =
study_icd_map |>
mutate(collected_all_disease_terms = str_trim(collected_all_disease_terms)) |>
mutate(collected_all_disease_terms = str_remove_all(collected_all_disease_terms, "^, "))
study_icd_map =
study_icd_map |>
filter(icd10_code != "" & !is.na(icd10_code))
study_icd_map =
study_icd_map |>
tidyr::separate_longer_delim(icd10_code, delim = ", ") |>
tidyr::separate_longer_delim(icd10_code, delim = ",")
study_icd_map =
study_icd_map |>
group_by(collected_all_disease_terms) |>
summarise(icd10_code = str_flatten(unique(sort(icd10_code)),
collapse = ", ",
na.rm = T),
.groups = "drop")
study_icd_map =
study_icd_map |>
mutate(icd10_code_origin = "Inferred from similar studies")
disease_mapping =
rows_patch(disease_mapping,
study_icd_map,
unmatched = "ignore")Matching, by = "collected_all_disease_terms"disease_mapping |>
filter(is.na(icd10_code)) |>
nrow()[1] 495disease_mapping |>
group_by(icd10_code_origin) |>
summarise(n = n()) |>
arrange(desc(n))# A tibble: 13 × 2
icd10_code_origin n
<chr> <int>
1 UMLS term match (collected_all_disease_terms) 10995
2 ICD Description Match (collected_all_disease_terms) 9575
3 Study PheCode Mapping 6780
4 UMLS term match 4820
5 Study Provided 3961
6 ICD Description Match (DISEASE/TRAIT) 3945
7 Phecode Phenotype Match (collected_all_disease_terms) 2194
8 Manual Mapping (collected_all_disease_terms) 1172
9 Inferred from similar studies 899
10 Study PheCode (Manual Mapping) 875
11 Phecode Phenotype Match (DISEASE/TRAIT) 580
12 <NA> 495
13 Manual Mapping (DISEASE/TRAIT) 25disease_mapping =
disease_mapping |>
mutate(icd10_code = sub("^([^-]+)-\\1$", "\\1", icd10_code))
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "C50-C50.9",
replacement = "C50"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F30-F39.9",
replacement = "F30"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F99-F99.9",
replacement = "F99"
)
)disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F40 F41 F42",
replacement = "F40, F41, F42"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "G47.8. G47.9",
replacement = "G47.8, G47.9"
)
)disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "J09.X",
replacement = "J09"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "G40.A",
replacement = "G40"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "G20.A1",
replacement = "G20"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "G20.C",
replacement = "G20"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F32.A",
replacement = "F32"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "S06.0X",
replacement = "S06.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "S06.0XA",
replacement = "S06.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "S06.0A",
replacement = "S06.0"
)
) disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "A15-A19.9|A15-A19",
replacement = paste0("A", 15:19, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "A50-A64.9|A50-A64",
replacement = paste0("A", 50:64, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "B20-B24.9",
replacement = paste0("B", 20:24, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "C60-C63.9|C60-C63",
replacement = paste0("C", 60:63, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "D80-D89",
replacement = paste0("D", 80:89, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E00-E07.9|E00-E07",
replacement = paste0("E0", 0:7, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E08-E13",
replacement = "E08, E09, E10, E11, E12, E13"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F30-F39",
replacement = paste0("F", 30:39, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "G00-G99.9|G00-G99",
replacement = paste0(
paste0("G0", 0:9, collapse = ", "),
paste0("G", 10:99, collapse = ", "),
collapse = ","
)
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "I20-I25.9|I20-I25",
replacement = paste0("I", 20:25, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "I60-I69.9|I60-I69",
replacement = paste0("I", 60:69, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "K40-K46.9|K40-K46",
replacement = paste0("K", 40:46, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "L00-L08.9|L00-L08",
replacement = paste0("L0", 0:8, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "L00-L99.9|L00-L99",
replacement = paste0(paste0("L0", 0:9, collapse = ", "),
paste0("L", 10:99, collapse = ", "),
collapse = ","
)
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N20-N23.9|N20-N23",
replacement = paste0("N", 20:23, collapse = ", ")
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "X71-X83",
replacement = paste0("X", 71:83, collapse = ", ")
)
) disease_mapping =
disease_mapping |>
mutate(icd10_code = str_split(icd10_code, ",\\s*")) |>
tidyr::unnest(icd10_code)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "B37.49",
replacement = "B37.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E05.90",
replacement = "E05.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E11.319|E11.31|E11.329.9|E11.329.|E11.32|E11.3.",
replacement = "E11.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E11.3.",
replacement = "E11.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E13.621.|E13.62",
replacement = "E11.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E78.00",
replacement = "E78.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F10.10",
replacement = "F10.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F17.201.|F17.20",
replacement = "F17.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F430",
replacement = "F43.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "G47.00",
replacement = "G47.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H01.00|H01.09.",
replacement = "H01.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H01.09.",
replacement = "H01.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H029",
replacement = "H02.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H60.90",
replacement = "H60.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H60.90",
replacement = "H60.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H91.8X9.",
replacement = "H91.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H91.90",
replacement = "H91.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H93.299.|H93.29",
replacement = "H01"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "I70.20",
replacement = "I70.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "I82.409.|I82.40|I82.4",
replacement = "I82"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "J30.9",
replacement = "J30.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "J45.998.|J45.909.|J45.901.|J45.99|J45.90",
replacement = "J45.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "J98.457.6",
replacement = "J98.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "K05.30-31",
replacement = "K05.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "K29.70",
replacement = "K29.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "K59.00",
replacement = "K59.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "L08.89",
replacement = "L08.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M06.99|M06.90",
replacement = "M06.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M10.99",
replacement = "M10.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M10.99",
replacement = "M10.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M13.90|M13.94|M13.96|M13.97|M13.99",
replacement = "M13.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M19.07",
replacement = "M19.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M19.90|M19.91|M19.94|M19.97|M19.99",
replacement = "M19.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M25.50|M25.51|M25.55|M25.569.|M25.56|M25.571.|M25.57",
replacement = "M25.5"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M25.76|M25.77",
replacement = "M25.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M43.16",
replacement = "M43.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M47.80|M47.82|M47.86",
replacement = "M47.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M47.92|M47.96",
replacement = "M47.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M48.02|M48.06",
replacement = "M48.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M54.22",
replacement = "M54.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M54.30|M54.39",
replacement = "M54.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M54.56|M54.57|M54.59",
replacement = "M54.5"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M54.99",
replacement = "M54.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M65.34",
replacement = "M65.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M65.96",
replacement = "M65.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M72.04",
replacement = "M72.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M79.09",
replacement = "M79.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M79.65|M79.66|M79.67",
replacement = "M79.6"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M79.79",
replacement = "M79.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M79.86",
replacement = "M79.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M81.99",
replacement = "M81.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N390",
replacement = "N39.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N50.89",
replacement = "N50.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N52",
replacement = "F52"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N52.9",
replacement = "F52.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N814",
replacement = "N81.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "P29.12",
replacement = "P29.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R06.00|R06.09",
replacement = "R06.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R06.83",
replacement = "R06.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R07.89",
replacement = "R07.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R07.8|R07.9",
replacement = "R07"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R09.89",
replacement = "R09.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R10.30",
replacement = "R10.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R10.8|R10.9",
replacement = "R10"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R11.0",
replacement = "R11"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R13.10",
replacement = "R13"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R13.1",
replacement = "R13"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R14.0",
replacement = "R14"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R19.7",
replacement = "R19"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R29.898.|R29.89",
replacement = "R29.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R31.29",
replacement = "R31.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R31.2|R31.9",
replacement = "R31"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R53.82|R53.83|R5382",
replacement = "R53.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R53.8",
replacement = "R53"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R56.9",
replacement = "R56"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R73.09|R73.02",
replacement = "R73.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R80.9",
replacement = "R80"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R82.998.|R82.99",
replacement = "R82.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R871",
replacement = "R87.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R87.6",
replacement = "R87"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R87.61",
replacement = "R87.6"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T50.905.",
replacement = "T50.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T78.40",
replacement = "T78.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T780",
replacement = "T78.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T81.149.88",
replacement = "T81.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T81.815.013.",
replacement = "T81.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T84.84",
replacement = "T84.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T887",
replacement = "T88.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "U80",
replacement = "U82"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "W44.9",
replacement = "W44"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z86.79",
replacement = "Z86.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z87.09",
replacement = "Z87.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z87.39",
replacement = "Z87.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z87.42",
replacement = "Z87.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z87.828.",
replacement = "Z87.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z87.891.",
replacement = "Z87.8"
)
)
disease_mapping =
disease_mapping |>
distinct()other_icd10_desc =
data.frame(
icd10_code = c("A09.9",
"A41",
"B95",
"B96",
"B97",
"B98",
"C44",
"C79",
"C80.0",
"C80.9",
"C90",
"D07",
"D35",
"D37",
"D47",
"D48",
"E03",
"E04",
"E21",
"E23",
"E27",
"E61",
"E80",
"E87",
"E89",
"F05",
"F17",
"F41",
"F43.0",
"F53",
"G31",
"G45",
"G46",
"G62",
"G93",
"G99",
"H47",
"H50",
"H57",
"H83",
"H91",
"H92",
"H93",
"I08",
"I27",
"I27.2",
"I44",
"I45",
"I48.0",
"I49",
"I51",
"I62",
"I71",
"J15",
"J16",
"J34",
"J38",
"J69",
"J84",
"J95",
"J96",
"K05",
"K07",
"K08",
"K09",
"K10",
"K12",
"K13",
"K22",
"K22.7",
"K52",
"K56",
"K64",
"K64.0",
"K64.9",
"K74",
"K75",
"K85.9",
"K86",
"K91",
"K91.8",
"K92",
"L02",
"L13",
"L30",
"L65",
"L73",
"L85",
"L89.1",
"L98",
"M05",
"M06",
"M07",
"M11",
"M13",
"M18",
"M19",
"M24",
"M25",
"M31",
"M35",
"M43",
"M48",
"M53",
"M62",
"M66",
"M67",
"M71",
"M77",
"M79",
"M79.7",
"M80",
"M81",
"M85",
"M89",
"M96",
"N02",
"N18.3",
"N18.4",
"N28",
"N39",
"N48",
"N73",
"N76",
"N88",
"N89",
"N91",
"N92",
"N93",
"N94",
"N99",
"O14",
"O04",
"O26",
"O32",
"O34",
"O36",
"O68",
"O75",
"O99",
"R03",
"R07",
"R09",
"R10",
"R19",
"R29",
"R29.6",
"R39",
"R40",
"R47",
"R57",
"T95.8",
"W44",
"Y95",
"Z86.3",
"Z87.3",
"Z87.4",
"Z87.7",
"Z87.8",
"T85.8",
"Z91.0",
"Z88.9",
"Z88.8",
"Z88",
"Z92.6",
"N90",
"U82"
),
icd10_description = c("Gastroenteritis and colitis of unspecified origin",
"Other sepsis",
"Streptococcus and staphylococcus as the cause of diseases classified to other chapters",
"Other specified bacterial agents as the cause of diseases classified to other chapters",
"Viral agents as the cause of diseases classified to other chapters",
"Other specified infectious agents as the cause of diseases classified to other chapters",
"Other malignant neoplasms of skin",
"Secondary malignant neoplasm of other and unspecified sites",
"Malignant neoplasm, primary site unknown, so stated",
"Malignant neoplasm, primary site unspecified",
"Multiple myeloma and malignant plasma cell neoplasms",
"Carcinoma in situ of other and unspecified genital organs",
"Benign neoplasm of other and unspecified endocrine glands",
"Neoplasm of uncertain or unknown behaviour of oral cavity and digestive organs",
"Other neoplasms of uncertain or unknown behaviour of lymphoid, haematopoietic and related tissue",
"Neoplasm of uncertain or unknown behaviour of other and unspecified sites",
"Other hypothyroidism",
"Other nontoxic goitre",
"Hyperparathyroidism and other disorders of parathyroid gland",
"Hypofunction and other disorders of pituitary gland",
"Other disorders of adrenal gland",
"Deficiency of other nutrient elements",
"Disorders of porphyrin and bilirubin metabolism",
"Other disorders of fluid, electrolyte and acid-base balance",
"Postprocedural endocrine and metabolic disorders, not elsewhere classified",
"Delirium, not induced by alcohol and other psychoactive substances",
"Mental and behavioural disorders due to use of tobacco",
"Other anxiety disorders",
"Acute stress reaction",
"Mental and behavioural disorders associated with the puerperium, not elsewhere classified",
"Other degenerative diseases of nervous system, not elsewhere classified",
"Transient cerebral ischaemic attacks and related syndromes",
"Vascular syndromes of brain in cerebrovascular diseases",
"Other polyneuropathies",
"Other disorders of brain",
"Other disorders of nervous system in diseases classified elsewhere",
"Other disorders of optic [2nd] nerve and visual pathways",
"Other strabismus",
"Other disorders of eye and adnexa",
"Other diseases of inner ear",
"Other hearing loss",
"Otalgia and effusion of ear",
"Other disorders of ear, not elsewhere classified",
"Multiple valve diseases",
"Other pulmonary heart diseases",
"Other secondary pulmonary hypertension",
"Atrioventricular and left bundle-branch block",
"Other conduction disorders",
"Paroxysmal atrial fibrillation",
"Ventricular fibrillation and flutter",
"Complications and ill-defined descriptions of heart disease",
"Other nontraumatic intracranial haemorrhage",
"Aortic aneurysm and dissection",
"Bacterial pneumonia, not elsewhere classified",
"Pneumonia due to other infectious organisms, not elsewhere classified",
"Other disorders of nose and nasal sinuses",
"Diseases of vocal cords and larynx, not elsewhere classified",
"Pneumonitis due to solids and liquids",
"Other interstitial pulmonary diseases",
"Postprocedural respiratory disorders, not elsewhere classified",
"Respiratory failure, not elsewhere classified",
"Gingivitis and periodontal diseases",
"Dentofacial anomalies [including malocclusion]",
"Other disorders of teeth and supporting structures",
"Cysts of oral region, not elsewhere classified",
"Other diseases of jaws",
"Stomatitis and related lesions",
"Other diseases of lip and oral mucosa",
"Other diseases of oesophagus",
"Barrett oesophagus",
"Other noninfective gastroenteritis and colitis",
"Paralytic ileus and intestinal obstruction without hernia",
"Haemorrhoids and perianal venous thrombosis",
"First degree haemorrhoids",
"Haemorrhoids, unspecified",
"Fibrosis and cirrhosis of liver",
"Other inflammatory liver diseases",
"Acute pancreatitis, unspecified",
"Other diseases of pancreas",
"Postprocedural disorders of digestive system, not elsewhere classified",
"Other postprocedural disorders of digestive system, not elsewhere classified",
"Other diseases of digestive system",
"Cutaneous abscess, furuncle and carbuncle",
"Other bullous disorders",
"Other dermatitis",
"Other nonscarring hair loss",
"Other follicular disorders",
"Other epidermal thickening",
"Stage II decubitus ulcer",
"Other disorders of skin and subcutaneous tissue, not elsewhere classified",
"Seropositive rheumatoid arthritis",
"Other rheumatoid arthritis",
"Psoriatic and enteropathic arthropathies",
"Other crystal arthropathies",
"Other arthritis",
"Arthrosis of first carpometacarpal joint",
"Other arthrosis",
"Other specific joint derangements",
"Other joint disorders, not elsewhere classified",
"Other necrotizing vasculopathies",
"Other systemic involvement of connective tissue",
"Other deforming dorsopathies",
"Other spondylopathies",
"Other dorsopathies, not elsewhere classified",
"Other disorders of muscle",
"Spontaneous rupture of synovium and tendon",
"Other disorders of synovium and tendon",
"Other bursopathies",
"Other enthesopathies",
"Other soft tissue disorders, not elsewhere classified",
"Fibromyalgia",
"Osteoporosis with pathological fracture",
"Osteoporosis without pathological fracture",
"Other disorders of bone density and structure",
"Other disorders of bone",
"Postprocedural musculoskeletal disorders, not elsewhere classified",
"Recurrent and persistent haematuria",
"Chronic kidney disease, stage 3",
"Chronic kidney disease, stage 4",
"Other disorders of kidney and ureter, not elsewhere classified",
"Other disorders of urinary system",
"Other disorders of penis",
"Other female pelvic inflammatory diseases",
"Other inflammation of vagina and vulva",
"Other noninflammatory disorders of cervix uteri",
"Other noninflammatory disorders of vagina",
"Other noninflammatory disorders of vulva and perineum",
"Excessive, frequent and irregular menstruation",
"Other abnormal uterine and vaginal bleeding",
"Pain and other conditions associated with female genital organs and menstrual cycle",
"Postprocedural disorders of genitourinary system, not elsewhere classified",
"Pre-eclampsia",
"Medical abortion",
"Maternal care for other conditions predominantly related to pregnancy",
"Maternal care for known or suspected malpresentation of fetus",
"Maternal care for known or suspected abnormality of pelvic organs",
"Maternal care for other known or suspected fetal problems",
"Labour and delivery complicated by fetal stress [distress]",
"Other complications of labour and delivery, not elsewhere classified",
"Other maternal diseases classifiable elsewhere but complicating pregnancy, childbirth and the puerperium",
"Abnormal blood-pressure reading, without diagnosis",
"Pain in throat and chest",
"Other symptoms and signs involving the circulatory and respiratory systems",
"Abdominal and pelvic pain",
"Other symptoms and signs involving the digestive system and abdomen",
"Other symptoms and signs involving the nervous and musculoskeletal systems",
"Tendency to fall, not elsewhere classified",
"Other symptoms and signs involving the urinary system",
"Somnolence, stupor and coma",
"Speech disturbances, not elsewhere classified",
"Shock, not elsewhere classified",
"Other complications of internal prosthetic devices, implants and grafts, not elsewhere classified",
"Foreign body entering into or through eye or natural orifice",
"Nosocomial condition",
"Personal history of endocrine, nutritional and metabolic diseases",
"Personal history of diseases of the musculoskeletal system and connective tissue",
"Personal history of diseases of the genitourinary system",
"Personal history of congenital malformations, deformations and chromosomal abnormalities",
"Personal history of other specified conditions",
"Other complications of internal prosthetic devices, implants and grafts, not elsewhere classified",
"Personal history of allergy, other than to drugs and biological substances",
"Personal history of allergy to unspecified drugs, medicaments and biological substances",
"Personal history of allergy to other drugs, medicaments and biological substances
",
"Personal history of allergy to drugs, medicaments and biological substances",
"Personal history of chemotherapy for neoplastic disease",
"Other noninflammatory disorders of vulva and perineum",
"Resistance to betalactam antibiotics")
)manual_icd10_map <-
readxl::read_xlsx(here::here("data/icd/manual_disease_icd10_mappings.xlsx"))
icd10_descriptions =
phecodes |>
select(icd10_code = ICD10,
icd10_description = ICD_DESCRIPTION
) |>
distinct()
# Expand multiple ICD codes into rows
to_add_expanded <- manual_icd10_map |>
mutate(icd10_code = str_split(icd10_code, ",\\s*")) |>
tidyr::unnest(icd10_code)
icd10_descriptions =
bind_rows(
icd10_descriptions,
to_add_expanded |>
select(icd10_code,
icd10_description = icd10_desc),
other_icd10_desc
)
icd10_descriptions = icd10_descriptions |> distinct()
icd10_descriptions =
icd10_descriptions |>
group_by(icd10_code) |>
summarise(icd10_description =
str_flatten(unique(icd10_description), collapse = "; ", na.rm = T),
.groups = "drop"
)
disease_mapping =
left_join(disease_mapping,
icd10_descriptions,
by = "icd10_code",
relationship = "many-to-one",
na_matches = "never"
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R871",
replacement = "R87"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_description =
ifelse(icd10_code == "R87",
"Abnormal findings in specimens from female genital organs",
icd10_description)
) # check if any ICD10 codes are missing descriptions
disease_mapping |>
filter(is.na(icd10_description)) |>
head()# A tibble: 6 × 9
`DISEASE/TRAIT` collected_all_diseas…¹ PUBMED_ID YEAR STUDY_ACCESSION
<chr> <chr> <int> <int> <chr>
1 smoking interaction in… lung cancer 29059373 2017 GCST005910
2 smoking interaction in… lung cancer 29059373 2017 GCST005909
3 smoking interaction in… lung cancer 29059373 2017 GCST005911
4 breast cancer (estroge… breast cancer 29058716 2017 GCST005076
5 breast cancer breast cancer 29058716 2017 GCST005077
6 breast cancer in brca1… breast cancer 29058716 2017 GCST005075
# ℹ abbreviated name: ¹collected_all_disease_terms
# ℹ 4 more variables: icd10_code <chr>, icd10_code_origin <chr>, phecode <dbl>,
# icd10_description <chr>gwas_study_info |>
filter(grepl("ICD10 F05",
`DISEASE/TRAIT`)) |>
select(`DISEASE/TRAIT`, MAPPED_TRAIT, collected_all_disease_terms, PUBMED_ID) DISEASE/TRAIT
<char>
1: ICD10 F05: Delirium due to known physiological condition (Gene-based burden)
2: ICD10 F05.9: Delirium, unspecified (Gene-based burden)
3: ICD10 F05.9: Delirium, unspecified
4: ICD10 F05: Delirium due to known physiological condition
MAPPED_TRAIT collected_all_disease_terms PUBMED_ID
<char> <char> <int>
1: alcohol withdrawal delirium alcohol-related disorders 34662886
2: delirium delirium 34662886
3: delirium delirium 34662886
4: alcohol withdrawal delirium alcohol-related disorders 34662886disease_mapping |>
filter(icd10_code == "F05")# A tibble: 3 × 9
`DISEASE/TRAIT` collected_all_diseas…¹ PUBMED_ID YEAR STUDY_ACCESSION
<chr> <chr> <int> <int> <chr>
1 behavioral disturbance… atypical behavior 25897833 2015 GCST002863
2 icd10 f05: delirium du… alcohol-related disor… 34662886 2021 GCST90083772
3 icd10 f05: delirium du… alcohol-related disor… 34662886 2021 GCST90079786
# ℹ abbreviated name: ¹collected_all_disease_terms
# ℹ 4 more variables: icd10_code <chr>, icd10_code_origin <chr>, phecode <dbl>,
# icd10_description <chr># F05 refers to delirium not induced by alcohol and other psychoactive substances
# yet, the mapped trait is alcohol withdrawal delirium
# replace with delirium
disease_mapping =
disease_mapping |>
mutate(collected_all_disease_terms =
ifelse(icd10_code == "F05",
"delirium",
collected_all_disease_terms)
)
gwas_study_info =
gwas_study_info |>
mutate(MAPPED_TRAIT =
ifelse(grepl("ICD10 F05", `DISEASE/TRAIT`),
str_replace_all(collected_all_disease_terms,
pattern = "alcohol-related disorders",
replacement = "delirium"),
collected_all_disease_terms)
)disease_mapping =
disease_mapping |>
arrange(YEAR,
PUBMED_ID,
STUDY_ACCESSION,
collected_all_disease_terms,
icd10_code)
fwrite(disease_mapping,
here::here("output/icd_map/gwas_disease_to_icd10_mapping.csv")
)
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] jsonlite_2.0.0 httr_1.4.7 data.table_1.17.8 stringr_1.5.2
[5] dplyr_1.1.4 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] bit_4.6.0 compiler_4.3.1 renv_1.0.3 promises_1.3.3
[5] tidyselect_1.2.1 Rcpp_1.1.0 git2r_0.36.2 tidyr_1.3.1
[9] callr_3.7.6 later_1.4.4 jquerylib_0.1.4 readxl_1.4.5
[13] yaml_2.3.10 fastmap_1.2.0 here_1.0.1 R6_2.6.1
[17] generics_0.1.4 knitr_1.50 tibble_3.3.0 rprojroot_2.1.0
[21] bslib_0.9.0 pillar_1.11.1 rlang_1.1.6 utf8_1.2.6
[25] cachem_1.1.0 stringi_1.8.7 httpuv_1.6.16 xfun_0.53
[29] getPass_0.2-4 fs_1.6.6 sass_0.4.10 bit64_4.6.0-1
[33] cli_3.6.5 withr_3.0.2 magrittr_2.0.4 ps_1.9.1
[37] digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1 lifecycle_1.0.4
[41] vctrs_0.6.5 evaluate_1.0.5 glue_1.8.0 cellranger_1.1.0
[45] whisker_0.4.1 purrr_1.1.0 rmarkdown_2.30 tools_4.3.1
[49] pkgconfig_2.0.3 htmltools_0.5.8.1