Last updated: 2025-09-10
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genomics_ancest_disease_dispar/
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library(dplyr)
library(data.table)
library(stringr)source(here::here("code/get_term_descendants.R"))gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_group_l1.csv"))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 145
2 asthma 131
3 alzheimers disease 124
4 breast cancer 112
5 major depressive disorder 108
6 schizophrenia 103dim(n_studies_trait)[1] 2901 2diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l1_all_disease_terms[gwas_study_info$l1_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 2029test <- data.frame(trait = unique(diseases))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002129/descendants"
bone_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 232
[1] "\n Some example terms"
[1] "cancer affecting bone of limb skeleton"
[2] "bone marrow cancer"
[3] "bone sarcoma"
[4] "primary bone lymphoma"
[5] "adult extraskeletal osteosarcoma" bone_cancer_terms = stringr::str_replace_all(bone_cancer_terms,
"\\bcarcinoma",
"cancer")
bone_cancer_terms = c("malignant bone neoplasm",
bone_cancer_terms)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(bone_cancer_terms, collapse = "|"),
"bone cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_4007/descendants"
# maybe do uninary bladder cancer instead
bladder_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 33
[1] "\n Some example terms"
[1] "superficial urinary bladder cancer"
[2] "jewett-marshall bladder cancer"
[3] "urinary bladder small cell neuroendocrine carcinoma"
[4] "bladder urothelial carcinoma"
[5] "bladder squamous cell carcinoma" bladder_cancer_terms = stringr::str_replace_all(bladder_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(bladder_cancer_terms, collapse = "|"),
"bladder cancer"
)
)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"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = "invasive lobular cancer",
"breast cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
str_replace_all(l1_all_disease_terms,
"benign neoplasm of (.*?)(?=,|$)|benign neoplasm of (.*?) (.*?)(?=,|$)",
"benign neoplasm")
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
str_replace_all(l1_all_disease_terms,
"benign (.*?) neoplasm(?=,|$)|benign (.*?) (.*?) neoplasm(?=,|$)",
"benign neoplasm")
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
str_replace_all(l1_all_disease_terms,
"(.*?) benign neoplasm(?=,|$)|(.*?) (.*?) neoplasm(?=,|$)",
"benign neoplasm")
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
str_replace_all(l1_all_disease_terms,
"polyp of (.*?)(?=,|$)|polyp of (.*?) (.*?)(?=,|$)",
"benign neoplasm")
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
str_replace_all(l1_all_disease_terms,
"(?=,|^)(.*?) polyp(?=,|$)|(?=,|^)(.*?) (.*?) polyp (?=,|$)",
"benign neoplasm")
)
# https://my.clevelandclinic.org/health/diseases/21477-adenomas - benign
other_benign_neoplasms = c("adenomatous colon polyp",
"colorectal adenoma",
"pituitary gland adenoma",
"aldosterone-producing adenoma",
"female genital tract polyp",
"polyp"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
str_replace_all(l1_all_disease_terms,
paste0(other_benign_neoplasms, collapse = "|"),
"benign neoplasm")
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000326/descendants"
cns_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 173
[1] "\n Some example terms"
[1] "malignant jugulotympanic paraganglioma"
[2] "malignant adrenal gland pheochromocytoma"
[3] "central nervous system lymphoma"
[4] "central nervous system embryonal neoplasm"
[5] "oligoastrocytoma" cns_cancer_terms = stringr::str_replace_all(cns_cancer_terms,
"\\bcarcinoma",
"cancer")pattern = paste0(cns_cancer_terms, collapse = "|")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = pattern,
"central nervous system cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_4362/descendants"
cervical_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 37
[1] "\n Some example terms"
[1] "cervix endometrial stromal tumor" "cervix melanoma"
[3] "cervical alveolar soft part sarcoma" "epithelioid trophoblastic tumor"
[5] "cervical adenosquamous carcinoma" cervical_cancer_terms = stringr::str_replace_all(cervical_cancer_terms,
"\\bcarcinoma",
"cancer")
cervical_cancer_terms = c("cervical intraepithelial neoplasia grade 2/3",
"uterine cervical cancer in situ",
cervical_cancer_terms)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = "uterine cervical cancer in situ",
"cervical cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(cervical_cancer_terms, collapse = "|"),
"cervical cancer"
)
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = "uterine cervical cancer in situ",
"cervical 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")
colorectal_cancer_terms= c("metastatic colorectal cancer",
"rectum cancer",
colorectal_cancer_terms)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"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = "colorectal mucinous adenocarcinoma",
"colorectal cancer"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = "metachronous colorectal adenoma",
"colorectal cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0011962/descendants"
endometrial_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 23
[1] "\n Some example terms"
[1] "endometrioid stromal sarcoma"
[2] "endometrial carcinoma"
[3] "endometrioid stromal sarcoma of the cervix"
[4] "uterine corpus endometrial stromal sarcoma"
[5] "endometrioid stromal sarcoma of the vagina"# also: http://www.ebi.ac.uk/efo/EFO_1001514: endometrial endometrioid carcinoma
endometrial_cancer_terms = c("endometrial endometrioid carcinoma",
endometrial_cancer_terms)
endometrial_cancer_terms = stringr::str_replace_all(endometrial_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(endometrial_cancer_terms, collapse = "|"),
"endometrial cancer"
)
)esophageal_cancer_terms <- c("esophageal adenocarcinoma",
"esophageal squamous cell cancer")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(esophageal_cancer_terms, collapse = "|"),
"esophageal cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002236/descendants"
ocular_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 75
[1] "\n Some example terms"
[1] "metastatic malignant neoplasm in the eye"
[2] "eyelid cancer"
[3] "ocular melanoma"
[4] "eye lymphoma"
[5] "cornea cancer" ocular_cancer_terms = stringr::str_replace_all(ocular_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(ocular_cancer_terms, collapse = "|"),
"ocular cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"cancer of gallbladder and extrahepatic biliary tract",
"gallbladder and bilary tract cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
"nodular sclerosis hodgkin lymphoma",
"hodgkins lymphoma"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
"head and neck squamous cell cancer",
"head and neck cancer, squamous cell cancer"
))intestinal_cancer_terms <- c("small intestine cancer",
"small bowel cancer",
"small intestine 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 = c("renal cell carcinoma",
"clear cell renal carcinoma",
"clear cell renal cell carcinoma",
kidney_cancer_terms)
kidney_cancer_terms = stringr::str_replace_all(kidney_cancer_terms,
"\\bcarcinoma",
"cancer")
kidney_cancer_terms = stringr::str_replace_all(kidney_cancer_terms,
"renal cancer",
"kidney 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"
)
)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = "laryngeal squamous cell cancer|laryngeal cancer",
"larynx 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_0005570/descendants"
lip_oral_cavity_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 51
[1] "\n Some example terms"
[1] "squamous odontogenic tumor" "lip cancer"
[3] "gum cancer" "oral cavity carcinoma"
[5] "vestibule of mouth cancer" lip_oral_cavity_cancer_terms = stringr::str_replace_all(lip_oral_cavity_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(lip_oral_cavity_cancer_terms, collapse = "|"),
"lip and oral cavity 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")
liver_cancer_terms = c("hepatitis virus-related liver cancer",
liver_cancer_terms)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"
)
)
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = "hepatitis virus-related liver cancer",
"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_0008170/descendants"
ovarian_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 77
[1] "\n Some example terms"
[1] "malignant non-epithelial tumor of ovary"
[2] "malignant epithelial tumor of ovary"
[3] "familial ovarian cancer"
[4] "ovarian endometrioid adenocarcinofibroma"
[5] "ovarian neuroendocrine neoplasm" ovarian_cancer_terms = stringr::str_replace_all(ovarian_cancer_terms,
"\\bcarcinoma",
"cancer")
ovarian_cancer_terms = c("high grade serous ovarian cancer",
"high grade ovarian cancer",
"high grade ovarian cancers",
"ovarian endometrioid cancer", # http://www.ebi.ac.uk/efo/EFO_1001515 - ovarian edometrioid carcinoma
"ovarian serous cancer", # http://www.ebi.ac.uk/efo/EFO_1001516 - ovarian serous carcinoma
ovarian_cancer_terms
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(ovarian_cancer_terms, collapse = "|"),
"ovarian cancer"
)
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = "high grade ovarian cancer",
"ovarian cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0009831/descendants"
pancreatic_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 37
[1] "\n Some example terms"
[1] "pancreatic endocrine carcinoma"
[2] "pancreas sarcoma"
[3] "malignant exocrine pancreas neoplasm"
[4] "pancreas lymphoma"
[5] "pancreatic small cell neuroendocrine carcinoma"pancreatic_cancer_terms = stringr::str_replace_all(pancreatic_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(pancreatic_cancer_terms, collapse = "|"),
"pancreatic cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_10283/descendants"
prostate_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 21
[1] "\n Some example terms"
[1] "prostate small cell carcinoma" "adenosquamous prostate carcinoma"
[3] "prostate sarcoma" "prostate neuroendocrine neoplasm"
[5] "prostate lymphoma" prostate_cancer_terms = stringr::str_replace_all(prostate_cancer_terms,
"\\bcarcinoma",
"cancer")
prostate_cancer_terms = c("grade iii prostatic intraepithelial neoplasia",
"metastatic prostate cancer",
prostate_cancer_terms)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = paste0(prostate_cancer_terms, collapse = "|"),
"prostate cancer"
)
)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")
nhl_terms = c("central nervous system non-hodgkin lymphoma",
"lymphoblastic lymphoma",
"extranodal nasal nk/t cell lymphoma", # https://www.ebi.ac.uk/ols4/ontologies/ordo/classes/http%253A%252F%252Fwww.orpha.net%252FORDO%252FOrphanet_86879
"follicular lymphoma", # http://purl.obolibrary.org/obo/DOID_0050873
"marginal zone b-cell lymphoma",
"diffuse large b-cell lymphoma",
nhl_terms)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"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0009260/descendants"
non_melanoma_skin_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 11
[1] "\n Some example terms"
[1] "keratinocyte carcinoma"
[2] "basal cell carcinoma"
[3] "skin basal cell carcinoma"
[4] "skin basosquamous cell carcinoma"
[5] "salivary gland basal cell adenocarcinoma"non_melanoma_skin_cancer_terms = stringr::str_replace_all(non_melanoma_skin_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(non_melanoma_skin_cancer_terms, collapse = "|"),
"non-melanoma skin cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_0060119/descendants"
other_pharynx_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 16
[1] "\n Some example terms"
[1] "nasopharynx carcinoma" "oropharynx cancer"
[3] "hypopharynx cancer" "pharynx squamous cell carcinoma"
[5] "tonsillar fossa cancer" other_pharynx_cancer_terms = stringr::str_replace_all(other_pharynx_cancer_terms,
"\\bcarcinoma",
"cancer")
other_pharynx_cancer_terms = c("hypopharyngeal cancer",
other_pharynx_cancer_terms)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(other_pharynx_cancer_terms, collapse = "|"),
"other pharynx cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_10534/descendants"
stomach_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 32
[1] "\n Some example terms"
[1] "gastric liposarcoma" "gastric gastrinoma"
[3] "gastric teratoma" "stomach carcinoma"
[5] "malignant gastric germ cell tumor"stomach_cancer_terms = stringr::str_replace_all(stomach_cancer_terms,
"\\bcarcinoma",
"cancer")
stomach_cancer_terms = c(
"diffuse stomach cancer",
"gastric cancer",
stomach_cancer_terms
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(stomach_cancer_terms, collapse = "|"),
"stomach cancer"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = "diffuse stomach cancer",
"stomach cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = "cutaneous squamous cell cancer",
"squamous cell cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_1781/descendants"
thyroid_cancer_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 24
[1] "\n Some example terms"
[1] "thyroid sarcoma"
[2] "thyroid gland carcinoma"
[3] "thyroid lymphoma"
[4] "thyroid angiosarcoma"
[5] "thyroid gland mucoepidermoid carcinoma"thyroid_cancer_terms = stringr::str_replace_all(thyroid_cancer_terms,
"\\bcarcinoma",
"cancer")
thyroid_cancer_terms = c("differentiated thyroid cancer",
thyroid_cancer_terms)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(thyroid_cancer_terms, collapse = "|"),
"thyroid cancer"
)
)uterine_cancer_terms <- c("uterine corpus cancer",
"uterine adnexa cancer")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = paste0(uterine_cancer_terms, collapse = "|"),
"uterine cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"uveal melanoma|uveal melanoma disease severity|epithelioid cell uveal melanoma|choroidal melanoma",
"ocular melanoma"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"ocular melanoma disease severity",
"ocular melanoma"
))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 145
2 asthma 131
3 alzheimers disease 124
4 breast cancer 122
5 major depressive disorder 108
6 colorectal cancer 104dim(n_studies_trait)[1] 2722 2diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l1_all_disease_terms[gwas_study_info$l1_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
test <- data.frame(trait = unique(diseases))
length(unique(diseases))[1] 1875# 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 type 2 diabetes mellitus
10835 7093 922
coronary artery disease major depressive disorder benign neoplasm
514 471 430
alzheimers disease breast cancer asthma
422 404 357
schizophrenia
356 fwrite(gwas_study_info,
here::here("output/gwas_cat/gwas_study_info_group_l1_v2.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 data.table_1.17.8
[5] dplyr_1.1.4 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] compiler_4.3.1 renv_1.0.3 promises_1.3.3 tidyselect_1.2.1
[5] Rcpp_1.1.0 git2r_0.36.2 callr_3.7.6 later_1.4.2
[9] jquerylib_0.1.4 yaml_2.3.10 fastmap_1.2.0 here_1.0.1
[13] R6_2.6.1 generics_0.1.4 curl_6.4.0 knitr_1.50
[17] tibble_3.3.0 rprojroot_2.1.0 bslib_0.9.0 pillar_1.11.0
[21] rlang_1.1.6 utf8_1.2.6 cachem_1.1.0 stringi_1.8.7
[25] httpuv_1.6.16 xfun_0.52 getPass_0.2-4 fs_1.6.6
[29] sass_0.4.10 cli_3.6.5 withr_3.0.2 magrittr_2.0.3
[33] ps_1.9.1 digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1
[37] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.4 glue_1.8.0
[41] whisker_0.4.1 rmarkdown_2.29 tools_4.3.1 pkgconfig_2.0.3
[45] htmltools_0.5.8.1