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genomics_ancest_disease_dispar/
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| Rmd | c9602c7 | IJbeasley | 2025-09-08 | More grouping to match GBD |
library(dplyr)
library(data.table)
library(ggplot2)
library(stringr)gwas_study_info <- fread(here::here("output/gwas_study_info_trait_ontology_info_l1.csv"))gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms = l1_all_disease_terms)library(httr)
library(jsonlite)
get_descendants <- function(url){
terms <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
terms <- c(terms, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
terms = unlist(terms)
terms = stringr::str_trim(tolower(terms))
terms = unique(terms)
print("Number of terms collected:")
print(length(terms))
print("\n Some example terms")
print(terms[1:5])
return(terms)
}gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "acne",
"acne vulgaris"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "adhd",
"attention-deficit/hyperactivity disorder"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "alcohol-related disorders|alcohol and nicotine codependence",
"alcohol use disorders"
)
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "alcohol use disorder",
"alcohol use disorders"
)
)dementia <- c("aids dementia",
"dementia",
"frontotemporal dementia",
"lewy body dementia",
"vascular dementia",
"alzheimers disease"
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(dementia, collapse = "|"),
"alzheimer's disease and other dementias"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mesh/terms/http%253A%252F%252Fid.nlm.nih.gov%252Fmesh%252FD001008/descendants"
anxiety_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 15
[1] "\n Some example terms"
[1] "panic disorder" "obsessive-compulsive disorder"
[3] "neurotic disorders" "neurocirculatory asthenia"
[5] "phobic disorders" gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(anxiety_terms, collapse = "|"),
"anxiety disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anxiety disorder|anxiety measurement",
"anxiety disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anxiety",
"anxiety disorders"
)
)afib_terms <- c("atrial fibrillation",
"atrial flutter",
"post-operative atrial fibrillation")
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(afib_terms, collapse = "|"),
"atrial fibrillation and flutter"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "methamphetamine",
"amphetamine"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/cvdo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_3627/descendants"
aortic_aneurysm_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 6
[1] "\n Some example terms"
[1] "abdominal aortic aneurysm" "ruptured aortic aneurysm"
[3] "thoracic aortic aneurysm" "ruptured thoracic aortic aneurysm"
[5] "ruptured abdominal aortic aneurysm"gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(aortic_aneurysm_terms, collapse = "|"),
"aortic aneurysm"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "autism",
"autism spectrum disorders"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "blindness|color vision disorder|vision disorder|myopia|refractive error|hyperopia|astigmatism|corneal astigmatism|presbyopia|anisometropia|esotropia|on-accomodative esotropia|ccommodative esotropia",
"blindness and vision loss"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "cannabis dependence",
"cannabis use disorders"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "urinary bladder cancer, disease progression measurement|b;adder tumor",
"bladder cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "colorectal cancer",
"colon and rectum cancer"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "ocular melanoma|ocular cancer",
"eye cancer"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "hodgkins lymphoma",
"hodgkin lymphoma"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "non-hodgkins lymphoma",
"non-hodgkin lymphoma"
)
)resp_cancer_terms = c("lung cancer",
"bronchus cancer",
"respiratory system cancer"
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(resp_cancer_terms, collapse = "|"),
"tracheal, bronchus, and lung cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F328383001/descendants"
chronic_liver_disease_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 114
[1] "\n Some example terms"
[1] "chronic necrosis of liver"
[2] "chronic nonalcoholic liver disease"
[3] "chronic hepatitis"
[4] "progressive intrahepatic cholestasis"
[5] "pulmonary fibrosis, hepatic hyperplasia, bone marrow hypoplasia syndrome"gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(chronic_liver_disease_terms, collapse = "|"),
"cirrhosis and other chronic liver diseases"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "cocaine-related disorders",
"cocaine use disorders"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "depressive symptom measurement|major depressive disorder",
"depressive disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "depressive disorder",
"depressive disorders"
)
)gal_bile_terms = c("gallbladder disease",
"bile duct disorder",
"biliary tract disease")
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(gal_bile_terms, collapse = "|"),
"gallbladder and biliary diseases"
)
)diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l2_all_disease_terms) |>
unlist() |>
stringr::str_trim()
pregnancy_terms <- grep("pregnancy", diseases, value = T)
gyno_terms <- c("endometriosis","placenta disease", pregnancy_terms)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(gyno_terms, collapse = "|"),
"gynecological diseases"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "bulimia nervosa|anorexia nervosa|binge eating|eating disorder",
"eating disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anorexia",
"eating disorders"
)
)gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "headache disorder|cluster headache|migraine",
"headache disorders"
)
)== coronary artery disease (https://www.ncbi.nlm.nih.gov/books/NBK209964/)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "coronary artery disease",
"ischemic heart disease"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "opioid dependence|opioid use disorder",
"opioid use disorders"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "parkinsons disease",
"parkinson's disease"
)
)gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "heroin dependence|drug dependence|nictone dependence|substance abuse|drug misuse|alcohol use disorders delirium",
"other drug use disorders"
)
)gbd_data <- data.table::fread(here::here("data/gbd/IHME-GBD_2021_DATA-aa22a7fd-1.csv"))
diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l2_all_disease_terms) |>
unlist() |>
stringr::str_trim()
gbd_data$cause[!tolower(gbd_data$cause) %in% unique(diseases)] |> sort() [1] "Acute glomerulonephritis"
[2] "Alopecia areata"
[3] "Bacterial skin diseases"
[4] "Brain and central nervous system cancer"
[5] "Cardiomyopathy and myocarditis"
[6] "Drug use disorders"
[7] "Endocrine, metabolic, blood, and immune disorders"
[8] "Fungal skin diseases"
[9] "Gallbladder and biliary tract cancer"
[10] "Hemoglobinopathies and hemolytic anemias"
[11] "Idiopathic developmental intellectual disability"
[12] "Idiopathic epilepsy"
[13] "Inguinal, femoral, and abdominal hernia"
[14] "Interstitial lung disease and pulmonary sarcoidosis"
[15] "Low back pain"
[16] "Lower extremity peripheral arterial disease"
[17] "Malignant neoplasm of bone and articular cartilage"
[18] "Malignant skin melanoma"
[19] "Nasopharynx cancer"
[20] "Neck pain"
[21] "Neuroblastoma and other peripheral nervous cell tumors"
[22] "Non-rheumatic valvular heart disease"
[23] "Oral disorders"
[24] "Other cardiovascular and circulatory diseases"
[25] "Other chronic respiratory diseases"
[26] "Other digestive diseases (internal)"
[27] "Other malignant neoplasms"
[28] "Other mental disorders"
[29] "Other musculoskeletal disorders"
[30] "Other neoplasms"
[31] "Other neurological disorders"
[32] "Other sense organ diseases"
[33] "Other skin and subcutaneous diseases"
[34] "Paralytic ileus and intestinal obstruction"
[35] "Pruritus"
[36] "Pulmonary Arterial Hypertension"
[37] "Scabies"
[38] "Soft tissue and other extraosseous sarcomas"
[39] "Sudden infant death syndrome"
[40] "Tracheal, bronchus, and lung cancer"
[41] "Upper digestive system diseases"
[42] "Urinary diseases and male infertility"
[43] "Vascular intestinal disorders"
[44] "Viral skin diseases" diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l2_all_disease_terms) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 1588# make frequency table
freq <- table(as.factor(diseases))
# sort in decreasing order
freq_sorted <- sort(freq, decreasing = TRUE)
# show top N, e.g. top 10
head(freq_sorted, 10)
chronic kidney disease
109388 10828
hypertension type 2 diabetes mellitus
7097 922
depressive disorderss ischemic heart disease
607 514
breast cancer alzheimer's disease and other dementias
402 377
schizophrenia asthma
356 355 gwas_study_info <- fwrite(gwas_study_info,
here::here("output/gwas_study_info_trait_ontology_info_l2.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 stringr_1.5.1 ggplot2_3.5.2
[5] data.table_1.17.8 dplyr_1.1.4 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 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 callr_3.7.6
[9] later_1.4.2 jquerylib_0.1.4 scales_1.4.0 yaml_2.3.10
[13] fastmap_1.2.0 here_1.0.1 R6_2.6.1 generics_0.1.4
[17] curl_6.4.0 knitr_1.50 tibble_3.3.0 rprojroot_2.1.0
[21] RColorBrewer_1.1-3 bslib_0.9.0 pillar_1.11.0 rlang_1.1.6
[25] cachem_1.1.0 stringi_1.8.7 httpuv_1.6.16 xfun_0.52
[29] getPass_0.2-4 fs_1.6.6 sass_0.4.10 cli_3.6.5
[33] withr_3.0.2 magrittr_2.0.3 ps_1.9.1 grid_4.3.1
[37] digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1 lifecycle_1.0.4
[41] vctrs_0.6.5 evaluate_1.0.4 glue_1.8.0 farver_2.1.2
[45] whisker_0.4.1 rmarkdown_2.29 tools_4.3.1 pkgconfig_2.0.3
[49] htmltools_0.5.8.1