Last updated: 2025-09-06
Checks: 7 0
Knit directory:
genomics_ancest_disease_dispar/
This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20220216) was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version dc84680. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .DS_Store
Ignored: .Rproj.user/
Ignored: data/.DS_Store
Ignored: data/gwas_catalog/
Ignored: output/gwas_study_info_cohort_corrected.csv
Ignored: output/gwas_study_info_trait_corrected.csv
Ignored: output/gwas_study_info_trait_ontology_info.csv
Ignored: output/trait_ontology/
Ignored: renv/
Untracked files:
Untracked: analysis/disease_burden.qmd
Untracked: analysis/download_ontology.Rmd
Untracked: data/gbd/
Untracked: data/who/
Unstaged changes:
Modified: analysis/disease_inves_by_ancest.Rmd
Modified: analysis/trait_ontology_collapse.Rmd
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown
(analysis/non_ontology_trait_collapse.Rmd) and HTML
(docs/non_ontology_trait_collapse.html) files. If you’ve
configured a remote Git repository (see ?wflow_git_remote),
click on the hyperlinks in the table below to view the files as they
were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | dc84680 | IJbeasley | 2025-09-06 | Updating trait collapsing once again |
| html | 3584988 | IJbeasley | 2025-09-06 | Build site. |
| 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")
) |>
mutate(collected_all_disease_terms =
str_replace(collected_all_disease_terms,
"^susceptibility to (.*?) (.*?) measurement$", "\\1")
) |>
mutate(collected_all_disease_terms =
str_replace(collected_all_disease_terms,
"^susceptibility to (.*?) (.*?) infection$", "\\1")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
str_replace(collected_all_disease_terms,
"susceptibility to viral and mycobacterial infections",
"viral and mycobacterial infections")
) |>
mutate(collected_all_disease_terms =
str_replace(collected_all_disease_terms,
"susceptibility to strep throat",
"strep throat")
)
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,
"head and neck malignant neoplasia",
"head and neck cancer"
))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,
"nicotine dependence symptom count",
"nicotine dependence"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"nicotine withdrawal symptom count|nicotine withdrawal measurement",
"nicotine withdrawal"
))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,
"hepatitis a virus infection",
"hepatitis a infection"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"hepatitis b virus infection",
"hepatitis b infection"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"hepatitis c virus infection",
"hepatitis c infection"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"chronic hepatitis c virus infection",
"chronic hepatitis, hepatitis c infection"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"chronic hepatitis b virus infection",
"chronic hepatitis, hepatitis b infection"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"hepatitis virus-related liver cancer",
"hepatitis, liver cancer"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"hiv-1 infection",
"hiv infection"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"time to remission of covid-19 symptoms",
"covid-19"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"mumps virus infectious disease",
"mumps"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"rubella infection",
"rubella"
))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,
"psychosis predisposition measurement",
"psychosis predisposition")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"phototoxic dermatitis|skin sensitivity to sun",
"photosensitivity disease")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"stenosing tenosynovitis",
"tenosynovitis")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"systemic juvenile idiopathic arthritis|oligoarticular juvenile idiopathic arthritis|
polyarticular juvenile idiopathic arthritis",
"juvenile idiopathic arthritis")
)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,
"irritable bowel syndrome symptom measurement",
"irritable bowel syndrome"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"respiratory symptom change measurement" ,
"respiratory symptom measurement"
))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$collected_all_disease_terms)
n_studies_trait = gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(collected_all_disease_terms, PUBMED_ID) |>
dplyr::distinct() |>
dplyr::group_by(collected_all_disease_terms) |>
dplyr::summarise(n_studies = dplyr::n()) |>
dplyr::arrange(desc(n_studies))
head(n_studies_trait)# A tibble: 6 × 2
collected_all_disease_terms n_studies
<chr> <int>
1 type 2 diabetes mellitus 149
2 asthma 133
3 alzheimers disease 125
4 breast cancer 115
5 major depressive disorder 110
6 schizophrenia 106dim(n_studies_trait)[1] 2571 2diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 1812gwas_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 = 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)
}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"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = "breast cancer in situ",
"breast 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/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" url <- "http://www.ebi.ac.uk/ols4/api/ontologies/ncit/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCIT_C181162/descendants"
female_repro_carcinoma_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 801
[1] "\n Some example terms"
[1] "cervical carcinoma" "endometrial carcinoma"
[3] "ovarian carcinoma" "vulvar carcinoma"
[5] "gestational choriocarcinoma"female_repro_cancer_terms <- c(female_repro_cancer_terms,
female_repro_carcinoma_terms)
female_repro_cancer_terms = stringr::str_replace_all(female_repro_cancer_terms,
"\\bcarcinoma",
"cancer")
female_repro_cancer_terms = unique(female_repro_cancer_terms)
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/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"
)
)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/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000565/descendants"
leukemia_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 133
[1] "\n Some example terms"
[1] "chronic eosinophilic leukemia, not otherwise specified"
[2] "acute leukemia"
[3] "mast-cell leukemia"
[4] "lymphoid leukemia"
[5] "myeloid leukemia" leukemia_terms = stringr::str_replace_all(leukemia_terms,
"\\bcarcinoma",
"cancer")gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(leukemia_terms, collapse = "|"),
"leukemia"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005952/descendants"
nhl_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 93
[1] "\n Some example terms"
[1] "b-cell non-hodgkins lymphoma" "lymphoma, aids-related"
[3] "sezary's disease" "acute lymphoblastic leukemia"
[5] "gastric non-hodgkin lymphoma"nhl_terms = stringr::str_replace_all(leukemia_terms,
"\\bcarcinoma",
"cancer")gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(nhl_terms, collapse = "|"),
"non-hodgkins lymphoma"
)
)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"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_1001849/descendants"
staph_skin_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 15
[1] "\n Some example terms"
[1] "staphyloenterotoxemia" "staphylococcal pneumonia"
[3] "staphylococcus aureus infection" "staphylococcal toxemia"
[5] "staphylococcus aureus pneumonia"gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(staph_skin_terms, collapse = "|"),
"staphylococcal skin infections"
)
)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = "herpes simplex infection",
"herpesviridae infectious disease"
)
)url<- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0004720/descendants"
prion_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 13
[1] "\n Some example terms"
[1] "scrapie" "kuru"
[3] "inherited prion disease" "creutzfeldt jacob disease"
[5] "prp systemic amyloidosis" gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(prion_terms, collapse = "|"),
"prion disease"
)
)# juvenile absence epilepsy
#
# juvenile myoclonic epilepsyra_terms <- c("acpa-positive rheumatoid arthritis",
"acpa-negative rheumatoid arthritis")
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(ra_terms, collapse = "|"),
"rheumatoid arthritis"
)
)pd_terms <- c("secondary parkinson disease",
"young adult-onset parkinsonism",
"parkinsons disease")
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(pd_terms, collapse = "|"),
"parkinson disease"
)
)cleft_terms <- c("cleft lip",
"cleft palate")
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(cleft_terms, collapse = "|"),
"orofacial cleft"
)
)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = c("refractory celiac disease"),
"celiac disease"
)
)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = c("morbid obesity|metabolically healthy obesity"),
"obesity"
)
)diabetic_eye_terms <- c("diabetic maculopathy",
"diabetic macular edema",
"diabetic retinopathy",
"proliferative diabetic retinopathy",
"non-proliferative diabetic retinopathy",
"diabetes mellitus type 2 associated cataract")
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(diabetic_eye_terms, collapse = "|"),
"diabetic eye disease"
)
)
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = "age of onset of type 2 diabetes mellitus",
"type 2 diabetes mellitus"
)
)?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 125
5 major depressive disorder 110
6 schizophrenia 106dim(n_studies_trait)[1] 2436 2diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l1_all_disease_terms) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 1709# 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
922 471 444
schizophrenia breast cancer asthma
356 354 346
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