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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_disease_trait_filtered_v2.csv"))Level 1 disease grouping: - collapse disease causes, e.g. contact dermatitis due to nickel to contact dermatitis - collapse disease subtypes, e.g. bipolar I and bipolar II to bipolar disorder - collapse disease onset times, e.g. early-onset alzheimers disease and late-onset alzheimers disease to alzheimers disease - collapse disease stages - collapse disease complications, e.g. device complication, trauma complication to complication
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms = collected_all_disease_terms)diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms[gwas_study_info$collected_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern("herpes zoster, nervous system disease"),
"nervous system disease"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern("herpes zoster, psoriasis"),
"psoriasis"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern("herpes zoster, rheumatoid arthritis"),
"rheumatoid arthritis"
)
)disturb_senses_terms <- c("disturbances of sensation of smell and taste",
"abnormality of the sense of smell",
"ageusia")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(disturb_senses_terms),
"disturbances to senses"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("chronic kidney disease stage 5"),
"chronic kidney disease"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("stage 5 chronic kidney disease"),
"chronic kidney disease"
))disease_complication_terms = c("device complication",
"trauma complication",
"adverse effect",
"aseptic loosening"
)
pattern <- vec_to_grep_pattern(disease_complication_terms)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = pattern,
"complication"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001361/descendants"
pulmonary_arterial_hypertension_terms <- get_descendants(url)
pattern <- vec_to_grep_pattern(pulmonary_arterial_hypertension_terms)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = pattern,
"pulmonary arterial hypertension"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("post-operative atrial fibrillation"),
"atrial fibrillation, post-operative"
))
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F49436004/descendants"
atrial_fibrillation_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(atrial_fibrillation_terms),
"atrial fibrillation"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F5370000/descendants"
atrial_flutter_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(atrial_flutter_terms),
"atrial flutter"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F64715009/descendants"
hypertensive_heart_disease_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(hypertensive_heart_disease_terms),
"hypertensive heart disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/cvdo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_3394/descendants"
ischemic_heart_disease_terms <- get_descendants(url)
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F414545008/descendants"
ischemic_heart_disease_terms_snomed <- get_descendants(url)
ischemic_heart_disease_terms = c(ischemic_heart_disease_terms,
ischemic_heart_disease_terms_snomed
) |>
str_length_sort()
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(ischemic_heart_disease_terms),
"ischemic heart disease"
))Likely also add, as ICD10 I25.1, seems to be coronary artery disease And gbd includes this in ischemic heart disease
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001645/descendants"
coronary_artery_disease_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(coronary_artery_disease_terms),
#pattern = paste0(coronary_artery_disease_terms, collapse = "(?=,|$) |\\b"),
"coronary artery disease"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern("coronary artery disease"),
# "coronary artery disease",
"ischemic heart disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000612/descendants"
myocardial_infarction_terms <- get_descendants(url)
myocardial_infarction_terms <- c("subsequent st elevation \\(stemi\\) and non-st elevation \\(nstemi\\) myocardial infarction",
myocardial_infarction_terms
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(myocardial_infarction_terms),
#pattern = paste0(myocardial_infarction_terms, collapse = "(?=,|$) |\\b"),
"myocardial infarction"
)
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern("post-operative myocardial infarction"),
"myocardial infarction, post-operative"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern("myocardial infarction"),
"ischemic heart disease"
))to_fix <- c("non-st elevation ischemic heart disease",
"post-operative ischemic heart disease",
"st elevation ischemic heart disease",
"subsequent st elevation \\(stemi\\) and non-st elevation \\(nstemi\\) ischemic heart disease")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(to_fix),
#paste0(to_fix, collapse = "(?=,|$) |\\b"),
"ischemic heart disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0009551/descendants"
heart_valve_disease_terms <- get_descendants(url)
# make non-rheumatic
rheumatic_terms <- c("rheumatic pulmonary valve disease",
"rheumatic disease of mitral valve")
heart_valve_disease_terms <-
heart_valve_disease_terms[!heart_valve_disease_terms %in% rheumatic_terms]
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(heart_valve_disease_terms),
# pattern = paste0(heart_valve_disease_terms,
# collapse = "(?=,|$) |\\b"),
"heart valve disease"
)
)aortic_aneurysm_terms <- c("thoracic aortic aneurysm",
"abdominal aortic aneurysm"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(aortic_aneurysm_terms),
# pattern = paste0(aortic_aneurysm_terms, collapse = "(?=,|$) |\\b"),
"aortic aneurysm"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("bacterial endocarditis"),
"endocarditis"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0001638/descendants"
cardiomyopathy_terms <- get_descendants(url)
cardiomyopathy_terms <- c("chagas cardiomyopathy",
"ischemic cardiomyopathy",
"idiopathic cardiomyopathy",
"nonischemic cardiomyopathy",
"peripartum cardiomyopathy", #? maybe include in pregnancy
cardiomyopathy_terms
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(cardiomyopathy_terms),
# pattern = paste0(cardiomyopathy_terms, collapse = "(?=,|$) |\\b"),
"cardiomyopathy"
))
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms ,
pattern = vec_to_grep_pattern("\\bidiopathic cardiomyopathy\\b"),
"cardiomyopathy"
)
)hemorrhage_terms <- c("intracerebral hemorrhage",
"non-lobar intracerebral hemorrhage",
"lobar intracerebral hemorrhage",
"parenchymal hematoma")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(hemorrhage_terms),
# pattern = paste0(hemorrhage_terms, collapse = "(?=,|$) |\\b"),
"hemorrhagic stroke")
)
stroke_terms <- c("stroke outcome",
"large artery stroke",
"small vessel stroke",
"ischemic stroke",
"stroke disorder",
"cardioembolic stroke",
"hemorrhagic stroke",
"intracranial hemorrhage",
"subdural hemorrhage"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(stroke_terms),
# paste0(stroke_terms, collapse = "(?=,|$) |\\b"),
"stroke")
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("post-operative stroke"),
"post-operative, stroke")
)# studies in gwas catalog don't specify lower or upper extremity
# but most peripheral artery disease is in lower extremities
gwas_study_info =
gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("\\bperipheral artery disease|\\bperipheral arterial disease"),
"lower extremity peripheral arterial disease"
))carotid_artery_disease_terms <- c("carotid artery thrombosis",
"carotid atherosclerosis"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(carotid_artery_disease_terms),
# pattern = paste0(carotid_artery_disease_terms, collapse = "(?=,|$) |\\b"),
"carotid artery disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000537/descendants"
hypertension_terms <- get_descendants(url)
hypertension_terms = c("primary hypertension",
"chronic venous hypertension",
"portal hypertension",
hypertension_terms
)
hypertension_terms = hypertension_terms[!hypertension_terms %in%
c(pulmonary_arterial_hypertension_terms,
hypertensive_heart_disease_terms,
"pulmonary arterial hypertension",
"hypertensive heart disease"
)
]
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(hypertension_terms),
# pattern = paste0(hypertension_terms, collapse = "(?=,|$) |\\b"),
"hypertension"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(hypertension_terms),
# pattern = paste0(hypertension_terms, collapse = "(?=,|$) |\\b"),
"hypertension"
))bundle_branch_block_terms <- c("left bundle branch block",
"right bundle branch block",
"complete right bundle branch block"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(bundle_branch_block_terms),
"bundle branch block"
)
)heart_block_terms <- c("first degree atrioventricular block",
"second degree atrioventricular block",
"third-degree atrioventricular block",
"atrioventricular block",
"bundle branch block",
"complete right heart block",
"left heart block"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(heart_block_terms),
# pattern = paste0(heart_block_terms, collapse = "(?=,|$) |\\b"),
"heart block"
))tacycardia_terms <- c("paroxysmal tachycardia",
"ventricular tachycardia",
"supraventricular tachycardia",
"paroxysmal supraventricular tachycardia",
"paroxysmal ventricular tachycardia"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(tacycardia_terms),
# pattern = paste0(tacycardia_terms, collapse = "(?=,|$) |\\b"),
"tachycardia"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("sudden cardiac arrest"),
"cardiac arrest"
)
)other_cardiac_arrhythmia_terms <- c("ventricular fibrillation",
"ventricular arrhythmia",
"cardiac arrest",
"bradycardia",
"cardiac arrhythmia"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(other_cardiac_arrhythmia_terms),
# pattern = paste0(other_cardiac_arrhythmia_terms, collapse = "(?=,|$) |\\b"),
"other cardiac arrhythmias"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMP_0002127/descendants"
mp_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(mp_terms),
"abnormal cardiovascular system morphology"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0000831/descendants"
thrombosis_terms <- get_descendants(url)
thrombosis_terms <- c("abnormal thrombosis",
thrombosis_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(thrombosis_terms),
# pattern = paste0(thrombosis_terms, collapse = "(?=,|$) |\\b"),
"thrombotic disease"
)
)arterial_occlusion_terms <- c("cerebral artery occlusion",
"occlusion precerebral artery",
"small artery occlusion"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(arterial_occlusion_terms),
# pattern = paste0(arterial_occlusion_terms, collapse = "(?=,|$) |\\b"),
"arterial occlusion"
)
)other_vascular_disorder_terms <- c("skin vascular disease",
"peripheral vascular disease",
"vascular disease",
"vasculitis",
"arteritis")
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_vascular_disorder_terms),
"other vascular disorders"
)
)congestive_heart_failure_terms <- c("systolic heart failure",
"diastolic heart failure",
"cor pulmonale",
"congenital heart disease",
"chronic pulmonary heart disease"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(congestive_heart_failure_terms),
# pattern = paste0(congestive_heart_failure_terms, collapse = "(?=,|$) |\\b"),
"congestive heart failure"
))brain_infarction_terms <- c("cerebral infarction",
"mri defined brain infarct",
"small cerebral infarction"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(brain_infarction_terms),
# pattern = paste0(brain_infarction_terms, collapse = "(?=,|$) |\\b"),
"brain infarction"
))vascular_insufficiency_terms <- c("vascular insufficiency disorder",
"chronic venous insufficiency",
"chronic intestinal vascular insufficiency"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(vascular_insufficiency_terms),
# pattern = paste0(vascular_insufficiency_terms, collapse = "(?=,|$) |\\b"),
"vascular insufficiency"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0020064/descendants"
abnormal_total_eosinophil_count_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(abnormal_total_eosinophil_count_terms),
# pattern = paste0(abnormal_total_eosinophil_count_terms, collapse = "(?=,|$) |\\b"),
"abnormal total eosinophil count"
))pregnancy_loss_terms <- c("habitual abortion",
"incomplete abortion",
"spontaneous abortion",
"abortion",
"spontaneous loss of pregnancy",
"incomplete loss of pregnancy"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(pregnancy_loss_terms),
# paste0(pregnancy_loss_terms, collapse = "(?=,|$) |\\b"),
"loss of pregnancy"
))
# exact synonyms (to avoid partial matches
# https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_1001491?lang=engwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("asparaginase-induced acute pancreatitis"),
"acute pancreatitis"
))alcoholic_liver_disease_terms <- c("alcoholic liver cirrhosis",
"alcoholic fatty liver disease",
"alcoholic hepatitis"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(alcoholic_liver_disease_terms),
"alcoholic liver disease"
))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("early-onset alzheimers disease",
"late-onset alzheimers disease")),
"alzheimers disease"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("allergic contact dermatitis of eyelid"),
"allergic contact dermatitis"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("seasonal allergic rhinitis"),
"allergic rhinitis"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0015909/descendants"
aplastic_anemia_terms <- get_descendants(url)
aplastic_anemia_terms <- c("severe aplastic anemia",
aplastic_anemia_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(aplastic_anemia_terms),
"aplastic anemia"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("autoimmune pancreatitis type 1"),
"autoimmune pancreatitis"
)) url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0005129/descendants"
cataract_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(cataract_terms),
"cataract"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("charcot-marie-tooth disease type 1a, decreased fine motor function"),
"charcot-marie-tooth disease type 1a"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("charcot-marie-tooth disease type 1a, decreased walking ability"),
"charcot-marie-tooth disease type 1a"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("charcot-marie-tooth disease type 1a, gait imbalance"),
"charcot-marie-tooth disease type 1a, gait disturbance"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0012532/descendants"
chronic_pain_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(chronic_pain_terms),
"chronic pain"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("acute cholecystitis"),
"cholecystitis"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002182/descendants"
communication_disorder_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(communication_disorder_terms),
"communication disorder"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("post-operative delirium"),
"delirium, post-operative"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_2723/descendants"
dermatitis_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(dermatitis_terms),
"dermatitis"
))
# see: http://www.ebi.ac.uk/efo/EFO_0000274
eczema_terms <- c("atopic eczema",
"hand eczema",
"eczematoid dermatitis", # see: http://purl.obolibrary.org/obo/HP_0000964
"recalcitrant dermatitis" # assuming same as recalcitrant atopic dermatitis http://www.ebi.ac.uk/efo/EFO_1000651
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(eczema_terms),
"dermatitis"
))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 = vec_to_grep_pattern(diabetic_eye_terms),
"diabetic eye disease"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("diabetic polyneuropathy"),
"diabetic neuropathy"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("iron deficiency anemia"),
"deficiency anemia"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("delayed encephalopathy after acute poisoning"),
"encephalopathy, poisoning"
))
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("encephalopathy acute infection-induced"),
"encephalopathy"
))# from: http://www.ebi.ac.uk/efo/EFO_0004274
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("renal overload-type gout"),
"gout"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0003664/descendants"
hemolytic_anemia_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(hemolytic_anemia_terms),
"hemolytic anemia"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F193225000/descendants"
hereditary_progressive_muscular_dystrophy_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(hereditary_progressive_muscular_dystrophy_terms),
"hereditary progressive muscular dystrophy"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/hp/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0004299/children"
hernia_abdominal_wall_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(hernia_abdominal_wall_terms),
"hernia of the abdominal wall"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("primary hyperaldosteronism"),
"hyperaldosteronism"
))hyperlipidemia_terms <- c("hypercholesterolemia",
"familial hypercholesterolemia",
"familial hyperlipidemia"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(hyperlipidemia_terms),
"hyperlipidemia"
))inborn_error_metab <- c("inborn disorder of amino acid metabolism", # ICD9:270, ICD9:270.9
"inborn disorder of amino acid transport", # ICD9:270.0
"inborn disorder of porphyrin metabolism", # ? ebi suggests ... ICD10CM:E80.4 - doesn't seem right match, but close - E80 range likely captures it
"inborn carbohydrate metabolic disorder", # ICD9:271.8
"familial lipoprotein lipase deficiency", # ICD9:272.3
"lactose intolerance", # ICD10: E73
"hereditary hemochromatosis", # ICD10CM:E83.110, ICD9: 275.01
"alpha 1-antitrypsin deficiency", # ICD9:273.4
"urea cycle disorder", # ICD9CM:270.6
"gaucher disease", # ICD10CM:E75.22, ICD9:272.7
"plasma protein metabolism disease", # ? ICD9:273.8
"disorder of metabolite absorption and transport"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(inborn_error_metab),
"inborn errors of metabolism"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0004565/descendants"
intestinal_obstruction_terms <- get_descendants(url)
# also add: http://purl.obolibrary.org/obo/DOID_8437
intestinal_obstruction_terms = c(intestinal_obstruction_terms,
"intestinal impaction"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(intestinal_obstruction_terms),
"intestinal obstruction"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0003884/descendants"
kidney_disease_terms <- get_descendants(url)
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_disease_terms),
"chronic kidney disease"
))penile_disorder <- c("balanitis",
"balanoposthitis",
"priapism",
"phimosis",
"erectile dysfunction",
"leukoplakia of penis")
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(penile_disorder),
"penile disorder"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern(
c("phototoxic dermatitis",
"skin sensitivity to sun"
)),
"photosensitivity disease")
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_1001908/descendants"
phobic_disorder_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(phobic_disorder_terms),
"phobic disorder"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0009556/descendants"
mineral_metabolism_disorder_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(mineral_metabolism_disorder_terms),
"mineral metabolism disease"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern(
c("non-alcoholic steatohepatitis",
"non-alcoholic liver disease"
)
),
"non-alcoholic fatty liver disease"
))orofacial_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 = vec_to_grep_pattern(orofacial_cleft_terms),
"orofacial cleft"
))osteoarthritis_terms <- c("knee osteoarthritis",
"hip osteoarthritis",
"hand osteoarthritis",
"spine osteoarthritis",
"toe osteoarthritis"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(osteoarthritis_terms),
"osteoarthritis"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0009003/descendants"
ovarian_dysfunction_terms <- get_descendants(url)
ovarian_dysfunction_terms <- c(ovarian_dysfunction_terms,
"premature ovarian failure",
"premature ovarian insufficiency"
)
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_dysfunction_terms),
"ovarian dysfunction"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000278/descendants"
pancreatitis_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(pancreatitis_terms),
"pancreatitis"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_3388/descendants"
periodontal_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(periodontal_terms),
"periodontal disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0009607/descendants"
pituitary_gland_disease_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(pituitary_gland_disease_terms),
"pituitary gland disease"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005804/descendants"
polycythemia_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(polycythemia_terms),
"polycythemia"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("pulmonary embolism, pulmonary infarction"),
"pulmonary embolism"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("psychosis predisposition"),
"psychosis")
)retinopathy_terms <- c("chronic central serous retinopathy",
"central serous retinopathy"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(retinopathy_terms),
"retinopathy")
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_remove_all(l1_all_disease_terms,
"^ldh-related sciatica, |, ldh-related sciatica$"
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("sickle cell anemia"),
"sickle cell disease and related diseases")
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("methicillin-resistant staphylococcus aureus infection"),
"staphylococcus aureus infection"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000717/descendants"
scleroderma_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(scleroderma_terms),
"systemic scleroderma"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("stenosing tenosynovitis"),
"tenosynovitis")
)thrombocytopenia_terms <- c("thrombocytopenia 4",
"acquired thrombocytopenia",
"primary thrombocytopenia"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(thrombocytopenia_terms),
"thrombocytopenia"
))tinea_terms <- c("tinea pedis",
"tinea unguium",
"dermatophytosis"
)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(tinea_terms),
"tinea"
))gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
vec_to_grep_pattern("vitamin b12 deficiency"),
"vitamin b deficiency"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0000505/descendants"
visual_impairment_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(visual_impairment_terms),
"visual impairment"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/upheno/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0000539/descendants"
abnormal_refraction_terms <- get_descendants(url)
gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(l1_all_disease_terms,
pattern = vec_to_grep_pattern(abnormal_refraction_terms),
"abnormality of refraction"
))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.csv")
)
sessionInfo()