Last updated: 2025-09-06
Checks: 7 0
Knit directory:
genomics_ancest_disease_dispar/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 82b6e8a | IJbeasley | 2025-09-06 | Update trait collapsing |
| html | 13c5442 | IJbeasley | 2025-09-05 | Build site. |
| Rmd | b209d1f | IJbeasley | 2025-09-05 | Even more trait collapsing |
library(dplyr)
library(data.table)
library(ggplot2)
library(stringr)gwas_study_info <- fread(here::here("output/gwas_study_info_trait_ontology_info.csv"))# gwas_study_info |>
# dplyr::filter(DISEASE_STUDY == T) |>
# dplyr::filter(all_disease_terms == "") |>
# View()
n_studies_trait = gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(all_disease_terms, PUBMED_ID) |>
dplyr::distinct() |>
dplyr::group_by(all_disease_terms) |>
dplyr::summarise(n_studies = dplyr::n()) |>
dplyr::arrange(desc(n_studies))
head(n_studies_trait)# A tibble: 6 × 2
all_disease_terms n_studies
<chr> <int>
1 type 2 diabetes mellitus 148
2 major depressive disorder 110
3 alzheimer disease 108
4 schizophrenia 102
5 asthma 100
6 breast carcinoma 100dim(n_studies_trait)[1] 2722 2gwas_study_info$all_disease_terms = sub(",$", "", gwas_study_info$all_disease_terms)
gwas_study_info$all_disease_terms = stringr::str_trim(gwas_study_info$all_disease_terms)
# collapse more traits
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms = all_disease_terms) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
str_replace(collected_all_disease_terms,
"^susceptibility to (.*?) measurement$", "\\1")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove(collected_all_disease_terms, " symptom severity measurement")
) |>
mutate(collected_all_disease_terms =
stringr::str_remove(collected_all_disease_terms, " severity measurement| exacerbation measurement")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\bdependence\\s+measurement\\b",
"dependence")) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\ballergy\\s+measurement\\b",
"allergy")) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\baddiction\\s+measurement\\b",
"addiction")) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\baddiction\\s+measurement\\b",
"addiction")) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\bsyndrome\\s+measurement\\b",
"syndrome")) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\bdisorder\\s+measurement\\b",
"disorder")) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove(collected_all_disease_terms,
pattern = "age of onset of "))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove(collected_all_disease_terms,
pattern = "family history of "))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"\\bcarcinoma",
"cancer")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"triple-negative breast cancer",
"breast cancer"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"cutaneous melanoma",
"melanoma"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"uveal melanoma|uveal melanoma disease severity|epithelioid cell uveal melanoma|choroidal melanoma",
"ocular melanoma"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"alcohol dependence measurement",
"alcohol dependence"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"alcohol dependence|alcohol withdrawal|alcohol withdrawal delirium|alcohol abuse",
"alcohol-related disorders"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"cannabis dependence measurement",
"cannabis dependence"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"cocaine use disorder|cocaine dependence",
"cocaine-related disorders"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"influenza a (h1n1)",
"influenza"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"asthma exacerbation measurement",
"asthma"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"adult onset asthma|childhood onset asthma",
"asthma"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"asthma symptoms measurement",
"asthma"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"atopic asthma",
"asthma"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"asthma, asthma",
"asthma"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"chronic obstructive asthma",
"asthma"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"bipolar ii disorder|bipolar i disorder",
"bipolar disorder"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"insomnia measurement",
"insomnia"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"post-traumatic stress disorder symptom measurement",
"post-traumatic stress disorder"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"multiple sclerosis symptom measurement",
"multiple sclerosis"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"anxiety disorder measurement",
"anxiety disorder"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"agoraphobia symptom measurement",
"agoraphobia"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"autism spectrum disorder",
"autism")
) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"asperger syndrome",
"autism")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"attention deficit hyperactivity disorder",
"adhd"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"adhd symptom measurement",
"adhd")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"early-onset alzheimers disease|late-onset alzheimers disease",
"alzheimers disease"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"alzheimer's disease",
"alzheimers disease"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"family history of alzheimer’s disease",
"alzheimers disease"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"alzheimer disease",
"alzheimers disease"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"parkinson's disease symptom measurement",
"parkinsons disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"lewy body dementia measurement",
"lewy body dementia"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"sleep apnea measurement",
"sleep apnea"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"sleep apnea during non-rem sleep|sleep apnea during rem sleep",
"sleep apnea")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"contact dermatitis due to nickel",
"contact dermatitis"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"covid-19 symptoms measurement",
"covid-19")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"coronary atherosclerosis measurement",
"coronary atherosclerosis")
) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"allergic contact dermatitis of eyelid",
"allergic contact dermatitis"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"seasonal allergic rhinitis",
"allergic rhinitis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"tubal factor infertility",
"female infertility"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"azoospermia",
"male infertility"
) )gwas_study_info = gwas_study_info |>
rowwise() |>
mutate(
collected_all_disease_terms = paste0(
unique(unlist(stringr::str_split(collected_all_disease_terms, ", "))),
collapse = ", "
)
) |>
ungroup()
gwas_study_info$collected_all_disease_terms = stringr::str_trim(gwas_study_info$collected_all_disease_terms)
gwas_study_info$collected_all_disease_terms = sub(",$", "", gwas_study_info$collected_all_disease_terms)
n_studies_trait = gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(collected_all_disease_terms, PUBMED_ID) |>
dplyr::distinct() |>
dplyr::group_by(collected_all_disease_terms) |>
dplyr::summarise(n_studies = dplyr::n()) |>
dplyr::arrange(desc(n_studies))
head(n_studies_trait)# A tibble: 6 × 2
collected_all_disease_terms n_studies
<chr> <int>
1 type 2 diabetes mellitus 149
2 asthma 133
3 alzheimers disease 121
4 breast cancer 115
5 major depressive disorder 110
6 schizophrenia 106dim(n_studies_trait)[1] 2590 2diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 1829gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms = collected_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 = unique(terms)
print("Number of terms collected:")
print(length(terms))
print("\n Some example terms")
print(terms[1:5])
return(terms)
}breast_cancer_terms <- grep("breast cancer", unique(diseases), value = T)
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(breast_cancer_terms, collapse = "|"),
"breast cancer"
)
)url<- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002898/descendants"
skin_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 131
[1] "\n Some example terms"
[1] "sebaceous gland cancer" "eyelid cancer"
[3] "CD4+/CD56+ hematodermic neoplasm" "primary cutaneous lymphoma"
[5] "cutaneous melanoma" # plus skin carcinoma terms
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0009259/descendants"
skin_carcinoma_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 46
[1] "\n Some example terms"
[1] "skin appendage carcinoma" "vulvar seborrheic keratosis"
[3] "non-melanoma skin carcinoma" "skin carcinoma in situ"
[5] "eyelid carcinoma" skin_cancer_terms = c(skin_cancer_terms, skin_carcinoma_terms)
skin_cancer_terms = stringr::str_replace_all(skin_cancer_terms,
"\\bcarcinoma",
"cancer")
skin_cancer_terms = unique(skin_cancer_terms)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(skin_cancer_terms, collapse = "|"),
"skin cancer"
)
)male_repro_cancer_terms = c("metastatic prostate cancer",
"prostate cancer",
"scrotum cancer",
"epididymis cancer",
"penile cancer"
)
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(male_repro_cancer_terms, collapse = "|"),
"male reproductive organ cancer"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_120/descendants"
female_repro_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 252
[1] "\n Some example terms"
[1] "uterine cancer"
[2] "female reproductive endometrioid cancer"
[3] "ovarian cancer"
[4] "fallopian tube cancer"
[5] "paraurethral gland cancer" female_repro_cancer_terms = stringr::str_replace_all(female_repro_cancer_terms,
"\\bcarcinoma",
"cancer")
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(female_repro_cancer_terms, collapse = "|"),
"female reproductive organ cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002691/descendants"
liver_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 76
[1] "\n Some example terms"
[1] "carcinoma of liver and intrahepatic biliary tract"
[2] "calcifying nested epithelial stromal tumor of the liver"
[3] "liver lymphoma"
[4] "biliary tract cancer"
[5] "liver sarcoma" liver_cancer_terms = stringr::str_replace_all(liver_cancer_terms,
"\\bcarcinoma",
"cancer")gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(liver_cancer_terms, collapse = "|"),
"liver cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0008903/descendants"
lung_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 63
[1] "\n Some example terms"
[1] "Graham-Boyle-Troxell syndrome" "malignant superior sulcus neoplasm"
[3] "lung carcinoma" "lung hilum cancer"
[5] "lung lymphoma" lung_cancer_terms = stringr::str_replace_all(lung_cancer_terms,
"\\bcarcinoma",
"cancer")gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(lung_cancer_terms, collapse = "|"),
"lung cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0005575/descendants"
colorectal_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 106
[1] "\n Some example terms"
[1] "colorectal lymphoma" "colorectal carcinoma"
[3] "familial colorectal cancer" "malignant colon neoplasm"
[5] "rectal cancer" colorectal_cancer_terms = stringr::str_replace_all(colorectal_cancer_terms,
"\\bcarcinoma",
"cancer")gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(colorectal_cancer_terms, collapse = "|"),
"colorectal cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_263/descendants"
kidney_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 51
[1] "\n Some example terms"
[1] "malignant cystic nephroma" "kidney liposarcoma"
[3] "renal pelvis carcinoma" "congenital mesoblastic nephroma"
[5] "renal carcinoma" kidney_cancer_terms = stringr::str_replace_all(kidney_cancer_terms,
"\\bcarcinoma",
"cancer")gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(kidney_cancer_terms, collapse = "|"),
"kidney cancer"
)
)allergy_terms <- grep("allergy", unique(diseases), value = T)
allergic_terms <- grep("allergic", unique(diseases), value = T)
allergic_terms = allergic_terms[allergic_terms != "non-allergic rhinitis"]
eczema_terms <- grep("eczema", unique(diseases), value = T)
allergy_terms <- c(allergy_terms,
allergic_terms,
eczema_terms)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(allergy_terms, collapse = "|"),
"allergic disease"
)
)abscess_terms <- grep("abscess", unique(diseases), value = T)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(abscess_terms, collapse = "|"),
"abscess"
)
)?Maybe: could group further into hypersensitivity reaction disease (with drug hypersensitivity syndrome)
gwas_study_info = gwas_study_info |>
rowwise() |>
mutate(
l1_all_disease_terms = paste0(
unique(unlist(stringr::str_split(l1_all_disease_terms, ", "))),
collapse = ", "
)
) |>
ungroup()
gwas_study_info$l1_all_disease_terms = stringr::str_trim(gwas_study_info$l1_all_disease_terms)
gwas_study_info$l1_all_disease_terms = sub(",$", "", gwas_study_info$l1_all_disease_terms)
n_studies_trait = gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(l1_all_disease_terms, PUBMED_ID) |>
dplyr::distinct() |>
dplyr::group_by(l1_all_disease_terms) |>
dplyr::summarise(n_studies = dplyr::n()) |>
dplyr::arrange(desc(n_studies))
head(n_studies_trait)# A tibble: 6 × 2
l1_all_disease_terms n_studies
<chr> <int>
1 type 2 diabetes mellitus 149
2 asthma 133
3 breast cancer 127
4 alzheimers disease 121
5 major depressive disorder 110
6 schizophrenia 106dim(n_studies_trait)[1] 2500 2diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l1_all_disease_terms) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 1764# 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 hypertension
109388 10828 6995
type 2 diabetes mellitus major depressive disorder coronary artery disease
921 471 444
schizophrenia breast cancer asthma
356 353 346
covid-19
305
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] utf8_1.2.6 cachem_1.1.0 stringi_1.8.7 httpuv_1.6.16
[29] xfun_0.52 getPass_0.2-4 fs_1.6.6 sass_0.4.10
[33] cli_3.6.5 withr_3.0.2 magrittr_2.0.3 ps_1.9.1
[37] grid_4.3.1 digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1
[41] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.4 glue_1.8.0
[45] farver_2.1.2 whisker_0.4.1 rmarkdown_2.29 tools_4.3.1
[49] pkgconfig_2.0.3 htmltools_0.5.8.1