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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)
dim(n_studies_trait)diseases <- 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))
test <- data.frame(trait = unique(diseases))gwas_study_info |>
filter(grepl("astrocytoma", l1_all_disease_terms)) |>
pull(STUDY) |>
unique()
# all comes from one cancer study - so a central nervous system cancer
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(PUBMED_ID == "36810956",
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern("astrocytoma"),
"central nervous system cancer"
),
l1_all_disease_terms
)
)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)
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 = vec_to_grep_pattern(bone_cancer_terms),
"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)
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 = vec_to_grep_pattern(bladder_cancer_terms),
"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 = vec_to_grep_pattern(breast_cancer_terms),
"breast cancer"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern("breast cancer in situ"),
"breast cancer"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern("invasive lobular cancer"),
"breast cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F92017000/descendants"
benign_blood_vessel_terms <- get_descendants(url)
benign_blood_vessel_terms <- stringr::str_replace_all(benign_blood_vessel_terms,
"\\bcarcinoma",
"cancer")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern(benign_blood_vessel_terms),
"benign neoplasm")
)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",
"metachronous colorectal adenoma",
"adenomatous colon polyp",
"female genital tract polyp",
"\\bpolyp\\b",
"uterine leiomyoma",
"hepatic hemangioma",
"lobular capilliary hemangioma",
"hemangioma of subcutaneous tissue",
"benign prostatic hyperplasia",
"melanocytic nevus",
"hemangioma",
"lymphangioma",
"vestibular schwannoma",
"schwannoma",
"skin lipoma", # likely benign ...
"lipoma",
"hamartoma",
"seborrheic keratosis",
"actinic keratosis",
"keratosis",
"meningioma", # most are benign (80%)
"common wart",
"plantar wart",
"penile Fibromatosis"
)
other_benign_neoplasms = str_length_sort(other_benign_neoplasms)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern(other_benign_neoplasms),
"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)
cns_cancer_terms = stringr::str_replace_all(cns_cancer_terms,
"\\bcarcinoma",
"cancer")pattern = vec_to_grep_pattern(cns_cancer_terms)
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)
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 = vec_to_grep_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 = vec_to_grep_pattern(cervical_cancer_terms),
"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)
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 = vec_to_grep_pattern(colorectal_cancer_terms),
"colorectal cancer"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern("colorectal mucinous adenocarcinoma"),
"colorectal cancer"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_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)
# 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 = vec_to_grep_pattern(endometrial_cancer_terms),
"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 = vec_to_grep_pattern(esophageal_cancer_terms),
"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)
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 = vec_to_grep_pattern(ocular_cancer_terms),
"ocular cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("cancer of gallbladder and extrahepatic biliary tract"),
"gallbladder and biliary tract cancer"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
vec_to_grep_pattern("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 ,
vec_to_grep_pattern("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)
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,
vec_to_grep_pattern("renal cancer"),
"kidney cancer")gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern(kidney_cancer_terms),
"kidney cancer"
)
)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern =
vec_to_grep_pattern(
c("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)
leukemia_terms <- c("b-cell acute lymphoblastic leukemia with t\\(1;19\\)\\(q23;p13.3\\); e2a-pbx1 \\(tcf3-pbx1\\)",
leukemia_terms)
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 = vec_to_grep_pattern(leukemia_terms),
"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)
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 = vec_to_grep_pattern(lip_oral_cavity_cancer_terms),
"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)
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 = vec_to_grep_pattern(liver_cancer_terms),
"liver cancer"
)
)
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_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)
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 = vec_to_grep_pattern(lung_cancer_terms),
"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)
ovarian_cancer_terms = stringr::str_replace_all(ovarian_cancer_terms,
"\\bcarcinoma",
"cancer")
ovarian_cancer_terms = c("high grade serous ovarian cancer",
"high grade ovarian serous adenocarcinoma",
"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 = vec_to_grep_pattern(ovarian_cancer_terms),
"ovarian cancer"
)
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_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)
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 = vec_to_grep_pattern(pancreatic_cancer_terms),
"pancreatic cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0021089/descendants"
peripheral_nervous_system_cancer_terms <- get_descendants(url)
peripheral_nervous_system_cancer_terms = stringr::str_replace_all(peripheral_nervous_system_cancer_terms,
"\\bcarcinoma",
"cancer")gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern(peripheral_nervous_system_cancer_terms),
"peripheral nervous system 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)
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 = vec_to_grep_pattern(prostate_cancer_terms),
"prostate cancer"
)
)mesothelioma_terms = c("pleural mesothelioma",
"malignant pleural mesothelioma")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern(mesothelioma_terms),
"mesothelioma"
)
)neuroendo_terms <- c("pulmonary neuroendocrine tumor",
"small intestine neuroendocrine tumor",
"pancreatic neuroendocrine tumor",
"carcinoid tumor" #http://www.ebi.ac.uk/efo/EFO_0004243
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern(neuroendo_terms),
"neuroendocrine tumor"
)
)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)
nhl_terms = stringr::str_replace_all(nhl_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)
# also likely that reticulum cell sarcoma is NHL
# see; http://www.ebi.ac.uk/efo/EFO_0005287
# https://pubmed.ncbi.nlm.nih.gov/6328875/
nhl_terms = c("reticulum cell sarcoma",
nhl_terms)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern(nhl_terms),
"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)
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 = vec_to_grep_pattern(non_melanoma_skin_cancer_terms),
"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)
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 = vec_to_grep_pattern(other_pharynx_cancer_terms),
"other pharynx cancer"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_1001968/descendants"
soft_tissue_sarcoma_terms <- get_descendants(url)
soft_tissue_sarcoma_terms = stringr::str_replace_all(soft_tissue_sarcoma_terms,
"\\bcarcinoma",
"cancer")
soft_tissue_sarcoma_terms = c("kaposis sarcoma",
"iatrogenic kaposis sarcoma",
soft_tissue_sarcoma_terms)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern(soft_tissue_sarcoma_terms),
"soft tissue sarcoma"
)
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern("sarcoma, soft tissue sarcoma"),
"soft tissue sarcoma"
)
)# can be either bone or soft tissue sarcoma
# hard to tell from these studies:
gwas_study_info |>
filter(grepl("ewing", l1_all_disease_terms)) |>
select(PUBMED_ID, `DISEASE/TRAIT`, COHORT, STUDY)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)
stomach_cancer_terms = stringr::str_replace_all(stomach_cancer_terms,
"\\bcarcinoma",
"cancer")
stomach_cancer_terms = c(
"diffuse stomach cancer",
"gastric cancer",
"gastric intestinal type adenocarcinoma",
"gastric cardia cancer",
"cardia cancer",
stomach_cancer_terms
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern(stomach_cancer_terms),
"stomach cancer"
)
) |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_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 = vec_to_grep_pattern("cutaneous squamous cell cancer"),
"non-melanoma skin 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)
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 = vec_to_grep_pattern(thyroid_cancer_terms),
"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 = vec_to_grep_pattern(uterine_cancer_terms),
"uterine cancer"
)
)gwas_study_info |>
filter(l1_all_disease_terms == "brain neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "brain neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"central nervous system cancer",
l1_all_disease_terms
)
)
# still leaves one study (with Brain Tumor)
gwas_study_info |>
filter(l1_all_disease_terms == "brain neoplasm") |>
pull(PUBMED_ID) |>
unique()
# from paper sup tables, ICD-10 code of brain tumor term is C71 - malignant neoplasm of brain
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "brain neoplasm" &
PUBMED_ID == 34594039,
"central nervous system cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "breast neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "breast neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"breast cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "bone neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "bone neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"bone cancer",
l1_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "bone neoplasm" &
grepl("benign", `DISEASE/TRAIT`, ignore.case = T),
"benign neoplasm",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "cecal neoplasm") |>
pull(`DISEASE/TRAIT`)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "cecal neoplasm" &
grepl("malignant", `DISEASE/TRAIT`, ignore.case = T),
"colorectal cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "colonic neoplasm") |>
select(MAPPED_TRAIT, `DISEASE/TRAIT`, STUDY_ACCESSION) |>
distinct() |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("malignant|cancer", `DISEASE/TRAIT`, ignore.case = T) &
l1_all_disease_terms == "colonic neoplasm",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("colonic neoplasm"),
"colorectal cancer"),
l1_all_disease_terms
)
)
# also specific example where measuring rectal cancer vs colon cancer
gwas_study_info |>
filter(grepl("colonic neoplasm", l1_all_disease_terms)) |>
select(MAPPED_TRAIT, `DISEASE/TRAIT`, STUDY_ACCESSION) |>
distinct() |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(STUDY_ACCESSION == "GCST90179122",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("colonic neoplasm"),
"colorectal cancer"),
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "endometrial neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "endometrial neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"endometrial cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "neoplasm of esophagus") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "neoplasm of esophagus" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"esophageal cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "eye neoplasm") |>
pull(`DISEASE/TRAIT`)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "eye neoplasm" &
grepl("cancer", `DISEASE/TRAIT`, ignore.case = T),
"ocular cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "gallbladder neoplasm") |>
pull(`DISEASE/TRAIT`)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "gallbladder neoplasm" &
grepl("cancer", `DISEASE/TRAIT`, ignore.case = T),
"gallbladder and biliary tract cancer",
l1_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "gallbladder neoplasm" &
`DISEASE/TRAIT` == "Gallbladder adenomyomatosis",
"benign neoplasm",
l1_all_disease_terms
)
)
# also specific example where measuring sclerosing cholangitis & gallbladder cancer
gwas_study_info |>
filter(grepl("gallbladder neoplasm", l1_all_disease_terms)) |>
select(STUDY_ACCESSION, `DISEASE/TRAIT`)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(STUDY_ACCESSION == "GCST005857",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("gallbladder neoplasm"),
"gallbladder and biliary tract cancer"),
l1_all_disease_terms
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
"central nervous system cancer, glioma",
"central nervous system cancer"
))
gwas_study_info |>
filter(l1_all_disease_terms == "glioma") |>
select(MAPPED_TRAIT, MAPPED_TRAIT_URI, `DISEASE/TRAIT`) |>
distinct()
# assume where measure survival and glioma, it is cancer
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("survival", MAPPED_TRAIT, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
"glioma",
"central nervous system cancer"),
l1_all_disease_terms
)
)
# assme where measure is grade, it is cancer
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("grade", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
"glioma",
"central nervous system cancer"),
l1_all_disease_terms
)
)
# Adult diffuse glioma - assume maglignant
# https://pmc.ncbi.nlm.nih.gov/articles/PMC9245936/
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("adult diffuse", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
"glioma",
"central nervous system cancer"),
l1_all_disease_terms
)
)
gwas_study_info |>
filter(`DISEASE/TRAIT` == "Glioma (pediatric/youth onset)") |>
select(MAPPED_TRAIT, MAPPED_TRAIT_URI, `DISEASE/TRAIT`, STUDY_ACCESSION) |>
distinct()
# from paper; seems malignant
# https://pubmed.ncbi.nlm.nih.gov/31040135/
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(STUDY_ACCESSION == "GCST008912",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("glioma"),
"central nervous system cancer"),
l1_all_disease_terms
))
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(`DISEASE/TRAIT` == "Glioblastoma" & l1_all_disease_terms == "glioma",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("glioma"),
"central nervous system cancer"),
l1_all_disease_terms
))
# for pubmed id: 22886559
# majority (~90%) graded glioma, gliobastoma and Oligodendroglioma
# so assume malignant
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(PUBMED_ID == 22886559 & l1_all_disease_terms == "glioma",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("glioma"),
"central nervous system cancer"),
l1_all_disease_terms)
)
# for pubmed id: 29743610
# majority (~60%) are glioblastoma
# so assume malignant
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(PUBMED_ID == 29743610 & l1_all_disease_terms == "glioma",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("glioma"),
"central nervous system cancer"),
l1_all_disease_terms)
)
# for pubmed id: 36810956
# seems to primarily include high grade glioma
# so assume malignant
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(PUBMED_ID == 36810956 & l1_all_disease_terms == "glioma",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("glioma"),
"central nervous system cancer"),
l1_all_disease_terms)
)
# pubmed id: 30714141
# considers glioma cancer
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(PUBMED_ID == 30714141 & l1_all_disease_terms == "glioma",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("glioma"),
"central nervous system cancer"),
l1_all_disease_terms)
)
# pubmed id: 34319593
# considers glioma a maglignant tumor
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(PUBMED_ID == 34319593 & l1_all_disease_terms == "glioma",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("glioma"),
"central nervous system cancer"),
l1_all_disease_terms)
)gwas_study_info |>
filter(l1_all_disease_terms == "glottis neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "glottis neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"larynx cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "kidney neoplasm") |>
pull(`DISEASE/TRAIT`)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "kidney neoplasm" &
grepl("malignant|cancer", `DISEASE/TRAIT`, ignore.case = T),
"kidney cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "laryngeal neoplasm") |>
select(MAPPED_TRAIT, MAPPED_TRAIT_URI, `DISEASE/TRAIT`, STUDY_ACCESSION) |>
distinct()
# one study -
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(STUDY_ACCESSION == "GCST90041889",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("laryngeal neoplasm"),
"larynx cancer"),
l1_all_disease_terms
))gwas_study_info |>
filter(l1_all_disease_terms == "liver neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "liver neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"liver cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "lung neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "lung neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"lung cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "lymphoid neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "lymphoid neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"malignant lymphoid tumor",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "meningeal neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "meningeal neoplasm" &
grepl("benign", `DISEASE/TRAIT`, ignore.case = T),
"benign neoplasm",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "neoplasm of mature b-cells") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "neoplasm of mature b-cells" &
`DISEASE/TRAIT` == "Follicular lymphoma",
"non-hodgkins lymphoma",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "mouth neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "mouth neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"lip and oral cavity cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(grepl("myeloid neoplasm", l1_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "myeloid neoplasm" &
grepl("Myeloid leukemia", `DISEASE/TRAIT`, ignore.case = T),
"leukemia",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "neuroendocrine neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "neuroendocrine neoplasm" &
grepl("PheCode 209", `DISEASE/TRAIT`, ignore.case = T),
"neuroendocrine tumor",
l1_all_disease_terms
)
)
# ? to double check: neuroendocrine tumor is malignant
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "neuroendocrine neoplasm" &
grepl("neuroendocrine tumor", `DISEASE/TRAIT`, ignore.case = T),
"neuroendocrine tumor",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "ovarian neoplasm") |>
pull(`DISEASE/TRAIT`)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "ovarian neoplasm" &
grepl("malignant", `DISEASE/TRAIT`, ignore.case = T),
"ovarian cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "nasopharyngeal neoplasm") |>
pull(`DISEASE/TRAIT`)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "nasopharyngeal neoplasm" &
grepl("carcinoma|cancer|malignant", `DISEASE/TRAIT`, ignore.case = T),
"nasopharyngeal cancer",
l1_all_disease_terms
)
)
gwas_study_info |>
filter(grepl("nasopharyngeal neoplasm", l1_all_disease_terms)) |>
pull(`DISEASE/TRAIT`)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "nasopharyngeal neoplasm" &
grepl("nasopharyngeal carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"nasopharyngeal cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "pancreatic neoplasm") |>
pull(`DISEASE/TRAIT`)
# Intraductal papillary mucinous neoplasm of the pancreas is a benign precursor lesion
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "pancreatic neoplasm" &
STUDY_ACCESSION == "GCST90104145",
"benign neoplasm",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "sigmoid neoplasm") |>
pull(`DISEASE/TRAIT`)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "sigmoid neoplasm" &
grepl("malignant", `DISEASE/TRAIT`, ignore.case = T),
"colorectal cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "skin neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "skin neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"non-melanoma skin cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "stomach neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "stomach neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"stomach cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "testicular neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "testicular neoplasm" &
grepl("malignant", `DISEASE/TRAIT`, ignore.case = T),
"testicular cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "tongue neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "tongue neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"lip and oral cavity cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "uterine neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "uterine neoplasm" &
grepl("benign", `DISEASE/TRAIT`, ignore.case = T),
"benign neoplasm",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "urogenital neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "urogenital neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"urogenital cancer",
l1_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "urogenital neoplasm" &
grepl("benign", `DISEASE/TRAIT`, ignore.case = T),
"benign neoplasm",
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms == "vulvar neoplasm") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "vulvar neoplasm" &
grepl("malignant|cancer|carcinoma", `DISEASE/TRAIT`, ignore.case = T),
"vulvar cancer",
l1_all_disease_terms
)
)ocular_melanoma_terms <- c("uveal melanoma",
"uveal melanoma disease severity",
"epithelioid cell uveal melanoma",
"choroidal melanoma",
"ocular melanoma disease severity"
)
ocular_melanoma_terms = str_length_sort(ocular_melanoma_terms)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern(ocular_melanoma_terms),
"ocular melanoma"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("ocular melanoma disease severity"),
"ocular melanoma"
))gwas_study_info |>
filter(l1_all_disease_terms == "benign neoplasm, colorectal cancer") |>
select(MAPPED_TRAIT, `DISEASE/TRAIT`, STUDY_ACCESSION) |>
distinct()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(STUDY_ACCESSION == "GCST90093303",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("benign neoplasm, colorectal cancer"),
"colorectal cancer"),
l1_all_disease_terms
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("larynx cancer, pharynx cancer"),
"larynx cancer, other pharynx cancer"
))gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("cutaneous melanoma"),
"malignant melanoma of skin"
))gwas_study_info |>
filter(l1_all_disease_terms == "melanoma") |>
pull(`DISEASE/TRAIT`) |>
unique()
# checked UKB data field 40006 (ICD10 codes)
# https://biobank.ctsu.ox.ac.uk/ukb/field.cgi?id=40006
# malignant melanoma of skin includes:
# Malignant melanoma of trunk
# Malignant melanoma of upper limb, including shoulder
# Malignant melanoma of lower limb, including hip
# checked UKB data field 20001
# https://biobank.ctsu.ox.ac.uk/ukb/field.cgi?id=20001
# malignant melanoma is a subcategory of skin cancer
malignant_skin_melanoma <- c("ICD10 C43",
"survival in skin melanoma",
"Skin melanoma specific survival",
"malignant melanoma of skin",
"malignant melanoma of trunk",
"Malignant melanoma \\(UKB data field 20001\\)",
"malignant melanoma \\(UKB data field 20001_1059\\)",
"malignant melanoma of upper limb, including shoulder",
"malignant melanoma of lower limb, including hip",
"ICD10 D03", # skin melanoma in situ
"Melanoma in situ \\(UKB data field 40006\\)"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "melanoma" &
grepl(paste0(malignant_skin_melanoma, collapse = "|\\b"),
`DISEASE/TRAIT`,
ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("melanoma"),
"malignant melanoma of skin"),
l1_all_disease_terms
))
# UKBB malignant melanoma of skin
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "melanoma" &
grepl("UKBB", COHORT, ignore.case = T) &
grepl("malignant melanoma", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("melanoma"),
"malignant melanoma of skin"),
l1_all_disease_terms
))
# cutaneous melanoma in title
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "melanoma" &
grepl("\\bcutaneous melanoma", STUDY, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("melanoma"),
"malignant melanoma of skin"),
l1_all_disease_terms
))
gwas_study_info |>
filter(l1_all_disease_terms == "\\bmelanoma") |>
pull(`DISEASE/TRAIT`) |>
unique()
gwas_study_info |>
filter(l1_all_disease_terms == "\\bmelanoma") |>
pull(PUBMED_ID) |>
unique()
# Checking the clinical trials that make up pubmed id 27023328
# https://clinicaltrials.gov/study/NCT01153763 - cutaneous melanoma
# https://clinicaltrials.gov/study/NCT01266967 - not specified, likely skin melanoma by MeSH terms
# https://clinicaltrials.gov/study/NCT01227889 - not specified, likely skin melanoma by MeSH terms
# https://clinicaltrials.gov/study/NCT01584648 - cutaneous melanoma
# https://clinicaltrials.gov/study/NCT01597908 - cutaneous melanoma
# thus, likely malignant melanoma of skin
# for pubmed ID 21983785,
# seems likely malignant melanoma of skin
# as test in situ vs invasive, and use non-skin cancer controls
# https://pmc.ncbi.nlm.nih.gov/articles/PMC3227560/#SM
# for pubmed id: 23455637 - uses one of the same cohorts as 21983785 (genoMEL)
# thus likely malignant melanoma of skin
# https://pubmed.ncbi.nlm.nih.gov/23455637/
# for pubmed id: 21706340
# Cutaneous malignant melanoma
# therefore, malignant melanoma of skin
# pubmed id: 19578364 also uses GenoMEL consortium
# therefore, malignant melanoma of skin
# pubmed id: 18488026
# cutaneous malignant melanoma
# therefore, malignant melanoma of skin
# pubmed id: 21983787
# also uses GenoMEL consortium
# therefore, malignant melanoma of skin
# pubmed id: 28212542
# cutaneous melanoma
# therefore, malignant melanoma of skin
# pubmed id: 24980573
# skin cancer melanoma discussion
# therefore, malignant melanoma of skin
# pubmed id: 35626014
# not entirely clear, but likely malignant melanoma of skin
# pubmed id: 34724200
# "current study focused on melanomas of the skin"
# hence, malignant melanoma of skin
# pubmed id: 34290314
# lists ICD10 codes as C43 (malignant melanoma of skin)
# for melanoma - thus malignant melanoma of skin
# pubmed id: 36064556
# lists cutaneous melanoma
malignant_skin_melanoma_studies <- c(27023328,
21983785,
23455637,
21706340,
19578364,
18488026,
21983787,
28212542,
24980573,
35626014,
34724200,
34290314,
36064556)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(PUBMED_ID %in% malignant_skin_melanoma_studies &
grepl("\\bmelanoma", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("melanoma"),
"malignant melanoma of skin"),
l1_all_disease_terms
))
# honestly not sure of pubmed id: 32887889
# ? guess but likely malignant melanoma of skin
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(PUBMED_ID == 32887889 &
grepl("\\bmelanoma", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("melanoma"),
"malignant melanoma of skin"),
l1_all_disease_terms
))
# also not of pubmed id: 33409738
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(PUBMED_ID == 33409738 &
grepl("\\bmelanoma", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("melanoma"),
"malignant melanoma of skin"),
l1_all_disease_terms
))gwas_study_info |>
filter(grepl("in situ", l1_all_disease_terms)) |>
pull(l1_all_disease_terms) |>
unique()
# cervical cancer
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("uterine cervix cancer in situ"),
"cervical cancer"
))
gwas_study_info |>
filter(grepl("in situ", l1_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique()
# strictly speaking is unspecified skin cancer
# likely ICD10 DO4 is non-melanoma skin cancer
# PheCode 172.3 - maps to D04.9
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("in situ", l1_all_disease_terms) &
grepl("ICD10 D04|PheCode 172.3", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("skin cancer in situ"),
"non-melanoma skin cancer"),
l1_all_disease_terms
)
)
# in situ cancer -> to cancer
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "in situ cancer",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("in situ cancer"),
"cancer"),
l1_all_disease_terms
)
)gwas_study_info |>
filter(l1_all_disease_terms=="cancer") |>
select(`DISEASE/TRAIT`, l1_all_disease_terms) |>
head()
# ICD10 Z85.4: Personal history of malignant neoplasm of genital organs
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "cancer" &
grepl("ICD10 Z85.4", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("cancer"),
"urogenital cancer"),
l1_all_disease_terms
)
)
# ICD10 Z85.1: Personal history of malignant neoplasm of trachea, bronchus and lung
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "cancer" &
grepl("ICD10 Z85.1", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("cancer"),
"tracheal bronchus and lung cancer"),
l1_all_disease_terms
)
)
# ICD10 Z85.0: Personal history of malignant neoplasm of digestive organs
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "cancer" &
grepl("ICD10 Z85.0", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("cancer"),
"digestive system cancer"),
l1_all_disease_terms
)
)
# Cancer of intrathoracic organs (PheCode 164)
# Malignant neoplasm of retroperitoneum and peritoneum (PheCode 159.4)"
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "cancer" &
grepl("PheCode 164|PheCode 159.4", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("cancer"),
"peritoneum cancer, retroperitoneal cancer"),
l1_all_disease_terms
)
)
# Malignant neoplasm of other and ill-defined sites within the digestive organs and peritoneum (PheCode 159)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "cancer" &
grepl("PheCode 159$", `DISEASE/TRAIT`, ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("cancer"),
"digestive system cancer, peritoneum cancer"),
l1_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("peritoneum cancer"),
"peritoneal cancer"
))gwas_study_info |>
filter(l1_all_disease_terms == "bladder tumor") |>
pull(`DISEASE/TRAIT`) |>
unique()gwas_study_info |>
filter(grepl("squamous cell cancer", l1_all_disease_terms)) |>
select(`DISEASE/TRAIT`, l1_all_disease_terms) |>
distinct()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("lung cancer, squamous cell cancer"),
"lung cancer"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("esophageal cancer, squamous cell cancer"),
"esophageal cancer"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("head and neck cancer, squamous cell cancer"),
"head and neck cancer"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("head and neck cancer, pain, squamous cell cancer"),
"head and neck cancer, cancer pain"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("non-melanoma skin cancer, squamous cell cancer"),
"non-melanoma skin cancer"
))gwas_study_info |>
filter(grepl("female reproductive organ cancer", l1_all_disease_terms)) |>
select(`DISEASE/TRAIT`, l1_all_disease_terms) |>
distinct()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "female reproductive organ cancer" &
grepl("benign", `DISEASE/TRAIT`, ignore.case = T),
"benign neoplasm",
l1_all_disease_terms
)
)
gwas_study_info |>
filter(grepl("\\breproductive system cancer", l1_all_disease_terms)) |>
select(`DISEASE/TRAIT`, l1_all_disease_terms) |>
distinct()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(l1_all_disease_terms == "reproductive system cancer" &
grepl("female reproductive cancer", `DISEASE/TRAIT`, ignore.case = T),
"female reproductive organ cancer",
l1_all_disease_terms
)
)gwas_study_info |>
filter(grepl("\\bmale reproductive organ cancer", l1_all_disease_terms)) |>
select(`DISEASE/TRAIT`, l1_all_disease_terms) |>
distinct()gwas_study_info |>
filter(grepl("\\bsmall cell cancer", l1_all_disease_terms)) |>
select(`DISEASE/TRAIT`, l1_all_disease_terms) |>
distinct()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(`DISEASE/TRAIT` == "Small-cell lung cancer",
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("small cell cancer"),
"lung cancer"),
l1_all_disease_terms
)
)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
case_when(l1_all_disease_terms == "central nervous system cancer, nervous system cancer" ~ "central nervous system cancer",
TRUE ~ l1_all_disease_terms)
) gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
case_when(l1_all_disease_terms == "non-malignant skin melanoma skin cancer" ~ "non-melanoma skin cancer",
l1_all_disease_terms == "non-malignant melanoma of skin skin cancer" ~ "non-melanoma skin cancer",
TRUE ~ l1_all_disease_terms)
)
#
# gwas_study_info =
# gwas_study_info |>
# mutate(l1_all_disease_terms =
# stringr::str_replace_all(l1_all_disease_terms,
# "non-malignant skin melanoma skin cancer",
# "non-melanoma skin cancer"
# )
# ) gwas_study_info |>
filter(grepl("skin cancer", l1_all_disease_terms) &
!grepl("non-melanoma", l1_all_disease_terms)
) |>
select(STUDY,
`DISEASE/TRAIT`,
all_disease_terms,
l1_all_disease_terms) |>
distinct()
# make them listed under both malignant melanoma of skin and non-melanoma skin cancer
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("skin cancer", l1_all_disease_terms) &
!grepl("melanoma", l1_all_disease_terms),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("skin cancer"),
"malignant melanoma of skin, non-melanoma skin cancer"),
l1_all_disease_terms
)
)gwas_study_info |>
filter(grepl("lymphoma", l1_all_disease_terms) &
!grepl("hodgkin", l1_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique()
# PheCode 202.23 maps to ICD-9 200.1 Lymphosarcoma
# which as from: http://snomed.info/id/188498009, is a form of non-Hodgkin's lymphoma
# PheCode 202.24 code maps to ICD-9 200.6, Anaplastic large cell lymphoma a form of non-Hodgkin's lymphoma
# all ICD10 C83 codes are non-Hodgkin's lymphoma
# ICD10 C85.1 maps to PheCode 202.2 Non-Hodgkins lymphoma
nhl_terms <- c("B cell non-Hodgkin lymphoma",
"PheCode 202.23",
"PheCode 202.24",
"ICD10 C83",
"ICD10 C85.1"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("lymphoma", l1_all_disease_terms, ignore.case = T) &
!grepl("hodgkin", l1_all_disease_terms, ignore.case = T) &
grepl(paste0(nhl_terms, collapse = "|"),
`DISEASE/TRAIT`,
ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("lymphoma"),
"non-hodgkin lymphoma"),
l1_all_disease_terms
)
)
# Non-follicular lymphoma (UKB data field 40006) likely non-hodgkin lymphoma
# as ICD10 C83: Non-follicular lymphoma is non-hodgkin lymphoma
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("lymphoma", l1_all_disease_terms, ignore.case = T) &
!grepl("hodgkin", l1_all_disease_terms, ignore.case = T) &
grepl("Non-follicular lymphoma \\(UKB data field 40006\\)",
`DISEASE/TRAIT`,
ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("lymphoma"),
"non-hodgkin lymphoma"),
l1_all_disease_terms
)
)
# Cancer code, self-reported: lymphoma (UKB data field 20001_1047)
# includes both hodgkin and non-hodgkin lymphoma
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("lymphoma", l1_all_disease_terms, ignore.case = T) &
!grepl("hodgkin", l1_all_disease_terms, ignore.case = T) &
grepl("Cancer code, self-reported: lymphoma \\(UKB data field 20001_1047\\)",
`DISEASE/TRAIT`,
ignore.case = T),
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("lymphoma"),
"non-hodgkin lymphoma, hodgkin lymphoma"),
l1_all_disease_terms
)
)
# for pubmed id: 34594039
# from sup table 1;
# Malignant lymphoma Malignant_Lymphoma is defined PheCodes 201/202 CD2_NONFOLLICULAR_LYMPHOMA
# thus includes both hodgkin and non-hodgkin lymphoma
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("lymphoma", l1_all_disease_terms, ignore.case = T) &
!grepl("hodgkin", l1_all_disease_terms, ignore.case = T) &
PUBMED_ID == 34594039,
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("lymphoma"),
"non-hodgkin lymphoma, hodgkin lymphoma"),
l1_all_disease_terms
)
)
# pubmed id: 23349640
# includes both hodgkin and non-hodgkin lymphoma
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("lymphoma", l1_all_disease_terms, ignore.case = T) &
!grepl("hodgkin", l1_all_disease_terms, ignore.case = T) &
PUBMED_ID == 23349640,
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("lymphoma"),
"non-hodgkin lymphoma, hodgkin lymphoma"),
l1_all_disease_terms
)
)
# not entirely sure for pubmed id: 36344522
# perhaps need to read further in, but seems like it is both hodgkin and non-hodgkin lymphoma
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
ifelse(grepl("lymphoma", l1_all_disease_terms, ignore.case = T) &
!grepl("hodgkin", l1_all_disease_terms, ignore.case = T) &
PUBMED_ID == 36344522,
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("lymphoma"),
"non-hodgkin lymphoma, hodgkin lymphoma"),
l1_all_disease_terms
)
)gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
case_when(l1_all_disease_terms == "breast cancer, cancer, colorectal cancer, lung cancer, ovarian cancer, prostate cancer" ~
"breast cancer, colorectal cancer, lung cancer, ovarian cancer, prostate cancer",
TRUE ~ l1_all_disease_terms)
)gwas_study_info =
gwas_study_info |>
rowwise() |>
mutate(l1_all_disease_terms = paste0(sort(unique(unlist(strsplit(l1_all_disease_terms, ", ")))),
collapse = ", ")
) |>
ungroup()gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms = stringr::str_remove_all(l1_all_disease_terms, "^,|,$")
) |>
mutate(l1_all_disease_terms = stringr::str_trim(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)
dim(n_studies_trait)diseases <- 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))
# 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)fwrite(gwas_study_info,
here::here("output/gwas_cat/gwas_study_info_group_l1_v2.csv")
)
sessionInfo()