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library(dplyr)
library(stringr)
library(data.table)source(here::here("code/get_term_descendants.R"))# gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_group.csv"))
gwas_study_info <- data.table::fread(here::here("output/gwas_cat/gwas_study_cancer_group.csv"))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = "^post-operative |^postoperative"
))gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"spine psteoarthritis"
)
),
"spine osteoarthritis"
)
)Taking definitions etc. from: https://pmc-ncbi-nlm-nih-gov.ucsf.idm.oclc.org/articles/PMC8584626/
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "37271218",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "abnormality of the eye",
replacement = "uveitis, retinal vasculitis, chorioretinitis, papillitis"
),
collected_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "37271218",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "abnormality of the genital system",
replacement = "genital aphthosis"
),
collected_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "37271218",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "abnormal aortic morphology",
replacement = "arterial thrombosis, aortic aneurysm, aneurysm of pulmonary artery"
),
collected_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "37271218",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "abnormal venous morphology",
replacement = "venous thromboembolism, superficial thrombophlebitis"
),
collected_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "37271218",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "abnormality of the vasculature",
replacement = "arterial thrombosis, aortic aneurysm, aneurysm of pulmonary artery, venous thromboembolism, superficial thrombophlebitis"
),
collected_all_disease_terms
)
)# for pubmed id 21878436
# measuring Coronary restenosis, which is an outcome of Percutaneous coronary intervention (PCI)
# included / background traits for the relevant study GENetic DEterminants of Restenosis project (GENDER)
# are found:
# https://academic.oup.com/eurheartj/article/25/13/1163/465324?login=true#89258510
# stable angina
# silent ischaemia -> silent myocardial ischaemia
# non-ST-elevation acute coronary syndromes excl. acute ST-elevation myocardial infarction
# this includes:
# unstable angina,
# non-ST-elevation myocardial infarction (NSTEMI) within acute subendocardial myocardial infarction
# Acute ischemic heart disease, unspecified:
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "21878436",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "coronary restenosis",
replacement = "coronary restenosis, stable angina, silent myocardial ischaemia, unstable angina, acute subendocardial myocardial infarction, acute ischemic heart disease"
),
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()
diseases <- unique(diseases)
print(length(diseases))[1] 2166gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(`DISEASE/TRAIT` == "Blister (PheCode 911)",
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormal blistering of the skin"),
"blister"
),
collected_all_disease_terms
)
)gwas_study_info |>
filter(grepl(vec_to_grep_pattern("abnormality of the digestive system"),
collected_all_disease_terms,
perl = T)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Other abdominal problem"gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("abnormality of the digestive system")))gwas_study_info |>
filter(grepl("abnormality of skin pigmentation", collected_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique() [1] "Skin colour saturation"
[2] "Perceived skin darkness"
[3] "Skin pigmentation"
[4] "Non-melanoma skin cancer"
[5] "Skin luminance"
[6] "Skin red/green component"
[7] "Skin yellow/blue component"
[8] "25-hydroxyvitamin D levels x skin colour (very fair vs. fair) interaction"
[9] "25-hydroxyvitamin D levels x skin colour (very fair vs. light olive) interaction"
[10] "Skin colour - Brown (UKB data field 1717)"
[11] "Skin colour - Dark olive (UKB data field 1717)"
[12] "Skin colour - Fair (UKB data field 1717)"
[13] "Skin colour - Light olive (UKB data field 1717)"
[14] "Skin colour - Very fair (UKB data field 1717)"
[15] "Skin colour - Dark olive (UKB data field 1717) (Gene-based burden)"
[16] "Skin colour - Brown (UKB data field 1717) (Gene-based burden)"
[17] "Skin colour - Fair (UKB data field 1717) (Gene-based burden)"
[18] "Skin colour - Light olive (UKB data field 1717) (Gene-based burden)"
[19] "Skin colour - Very fair (UKB data field 1717) (Gene-based burden)"
[20] "Skin pigmentation traits"
[21] "Tatto pigmentation" # as can see, most of these traits are not about true skin pigmentation abnormalities
# just about skin pigmentation in general
# if `DISEASE/TRAIT` contains "UKB data field 1717" (which is just a skin colour measurment field)
# then remove "abnormality of skin pigmentation" from collected_all_disease_terms
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("UKB data field 1717",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_remove_all(collected_all_disease_terms,
pattern = "abnormality of skin pigmentation"
),
collected_all_disease_terms
)
)
# also remove if `DISEASE/TRAIT` contains "Tattoo pigmentation"
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("tattoo pigmentation|tatto pigmentation",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_remove_all(collected_all_disease_terms,
pattern = "abnormality of skin pigmentation"
),
collected_all_disease_terms
)
)
# also remove if `DISEASE/TRAIT` is any of the following:
# - Perceived skin darkness
# - Skin red/green component
# - Skin yellow/blue component
# - Skin pigmentation traits
# - Skin pigmentation
# - Skin luminance
remove_terms <- c("Perceived skin darkness",
"Skin red/green component",
"Skin yellow/blue component",
"Skin pigmentation traits",
"Skin pigmentation",
"Skin luminance",
"Skin colour saturation"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(`DISEASE/TRAIT` %in% remove_terms,
stringr::str_remove_all(collected_all_disease_terms,
pattern = "abnormality of skin pigmentation"
),
collected_all_disease_terms
)
)
# this leaves PUBMED_ID 23548203, which according to suplementary table 1
# is `Number of non-melanoma skin cancer (5+)`
# so change to "non-melanoma skin cancer"
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "23548203",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "abnormality of skin pigmentation",
replacement = "non-melanoma skin cancer"
),
collected_all_disease_terms
)
)# interesting things going on with abnormal thrombosis
gwas_study_info |>
filter(grepl(vec_to_grep_pattern("abnormal thrombosis"),
collected_all_disease_terms, perl = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms, PUBMED_ID) DISEASE/TRAIT
<char>
1: Thrombosis
2: Blood clot, DVT, bronchitis, emphysema, asthma, rhinitis, eczema, allergy diagnosed by doctor: PHESANT recoding (UKB data field 6152_100)
3: Blood clot, DVT, bronchitis, emphysema, asthma, rhinitis, eczema, allergy diagnosed by doctor: Blood clot in the lung (UKB data field 6152_7)
4: Blood clot in the lung (UKB data field 6152) (Gene-based burden)
5: Blood clot in the lung (UKB data field 6152)
collected_all_disease_terms PUBMED_ID
<char> <int>
1: abnormal thrombosis 26908601
2: abnormal thrombosis 34737426
3: abnormal thrombosis 34737426
4: abnormal thrombosis 34662886
5: abnormal thrombosis 34662886# if DISEASE/TRAIT contains Blood clot in the lung \\(UKB data field 6152\\)
# replace abnormal thrombosis in collected_all_disease_terms with pulmonary embolism
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Blood clot in the lung \\(UKB data field 6152\\)",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormal thrombosis"),
"pulmonary embolism"
),
collected_all_disease_terms
)
)
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Blood clot in the lung \\(UKB data field 6152_7\\)",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormal thrombosis"),
"pulmonary embolism"
),
collected_all_disease_terms
)
)
## PHESANT recoding (UKB data field 6152_100)
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("PHESANT recoding \\(UKB data field 6152_100\\)",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormal thrombosis, allergic disease, respiratory system disease"),
"pulmonary embolism, deep vein thrombosis, chronic bronchitis, emphysema, asthma, rhinitis, eczema"
),
collected_all_disease_terms
)
)
# for pubmed id: 26908601
# remove abnormal thrombosis
# because this is included in the other provided terms
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "26908601",
stringr::str_remove_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormal thrombosis")
),
collected_all_disease_terms
)
)# for pubmed id 28753643
# acute coronary syndrome (ACS)
# comes from the SOLID-TIMI 52 cohort: experienced acute coronary syndrome (ACS; unstable angina, non–ST-elevation or ST-elevation MI)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "28753643",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "acute coronary syndrome",
replacement = "unstable angina, acute subendocardial myocardial infarction, acute transmural myocardial infarction of unspecified site"
),
collected_all_disease_terms
)
)
# define similarly in pubmed id: 24952865, 25583994, 25935875
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID %in% c("28753643","24952865", "28753645", "25583994", "25935875", "34158603"),
stringr::str_replace_all(collected_all_disease_terms,
pattern = "acute coronary syndrome",
replacement = "unstable angina, acute subendocardial myocardial infarction, acute transmural myocardial infarction of unspecified site"
),
collected_all_disease_terms
)
)
# for pubmed id 35356681, acute coronary syndrome (ACS) - is actually non-ST elevation acute coronary syndrome
gwas_study_info |>
filter(grepl(vec_to_grep_pattern("acute coronary syndrome"),
collected_all_disease_terms,
perl = T)) |>
filter(PUBMED_ID == "35356681") |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Bisoprolol clearance in non-ST elevation acute coronary syndrome"gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "35356681",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "acute coronary syndrome",
replacement = "acute subendocardial myocardial infarction"
),
collected_all_disease_terms
)
)gwas_study_info |>
filter(grepl("attached earlobe", collected_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Common traits (Other)" "Earlobe attachment" # remove attached earlobe
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = "attached earlobe"
))gwas_study_info |>
filter(grepl(vec_to_grep_pattern("chronic disease"),
collected_all_disease_terms,
perl = T)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Long standing illness disability or infirmity (UKB data field 2188)"
[2] "Long standing illness disability or infirmity (UKB data field 2188) (Gene-based burden)"gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("chronic disease")))gwas_study_info |>
filter(grepl("facial wrinkling", collected_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Facial wrinkles"
[2] "Facial wrinkles (forehead)"
[3] "Facial wrinkles (frown lines)"
[4] "Facial wrinkles (crow's feet)"
[5] "Facial wrinkles (principal components analysis)"
[6] "Facial wrinkles (under eye)" # remove facial wrinkling
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = "facial wrinkling"
))gwas_study_info |>
filter(grepl(vec_to_grep_pattern("fibrosis"),
collected_all_disease_terms,
perl = T)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Fibrosis"
[2] "Fibrosis (moderate to severe) in head and neck cancer treated with radiotherapy"
[3] "Fibrosis (severe) in head and neck cancer treated with radiotherapy"
[4] "Fibrosis or atrophy (moderate to severe) in head and neck cancer treated with radiotherapy"
[5] "Fibrosis or atrophy (severe) in head and neck cancer treated with radiotherapy"
[6] "Standardised Total Average Toxicity (late dysphagia, xerostomia, fibrosis or atrophy) in head and neck cancer treated with radiotherapy"
[7] "Standardised Total Average Toxicity (acute dysphagia, mucositis, late dysphagia, xerostomia, fibrosis or atrophy) in head and neck cancer treated with radiotherapy"gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("fibrosis, head and neck cancer"),
replacement = "head and neck cancer"
)
)
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "38601445",
str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("fibrosis"),
replacement = "lung cancer"
),
collected_all_disease_terms
)
)gwas_study_info |>
filter(grepl(vec_to_grep_pattern("formal thought disorder"),
collected_all_disease_terms,
perl = T)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Formal thought disorder in schizophrenia"
[2] "Positive formal thought disorder in major depressive disorder, bipolar disorder or schizophrenia spectrum disorders"# as formal thought disorder is within other psychiatric traits
# remove
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("formal thought disorder")))gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("childhood gender nonconformity"),
"gender identity disorder"
))
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = "gender identity disorder"
))
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = "sexual and gender identity disorders"
))gwas_study_info |>
filter(grepl("handedness", collected_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique() [1] "Handedness (non-right-handed vs right-handed)"
[2] "Handedness (Left-handed vs. non-left-handed)"
[3] "Handedness (left-handed vs. right-handed)"
[4] "Relative hand skill in reading disability"
[5] "Relative hand skill"
[6] "Handedness in dyslexia"
[7] "Handedness"
[8] "Handedness (chirality/laterality): Right-handed (UKB data field 1707_1)"
[9] "Handedness (Right-handed vs. non-right-handed)"
[10] "Ambidextrousness"
[11] "Ambidextrousness (ambidextrous vs right-handed)"
[12] "Left-handedness"
[13] "Handedness (confirmatory factor analysis Factor 36)" # remove handedness
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = "handedness"
))
# also remove functional laterality if Handedness chirality laterality is in DISEASE/TRAIT
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Handedness",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_remove_all(collected_all_disease_terms,
pattern = "functional laterality"
),
collected_all_disease_terms
)
)
# also remove functional laterality if Usual side of head for mobile phone use is in DISEASE/TRAIT
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Usual side of head for mobile phone use",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_remove_all(collected_all_disease_terms,
pattern = "functional laterality"
),
collected_all_disease_terms
)
)
# also remove functional laterality if PUBMED_ID=20585627
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "20585627",
stringr::str_remove_all(collected_all_disease_terms,
pattern = "functional laterality"
),
collected_all_disease_terms
)
) gwas_study_info |>
filter(grepl(vec_to_grep_pattern("hyperplasia"),
collected_all_disease_terms,
perl = T)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Bilateral adrenal hyperplasia"gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Bilateral adrenal hyperplasia",
`DISEASE/TRAIT`,
ignore.case = TRUE),
str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("hyperplasia"),
replacement = "bilateral adrenal hyperplasia"
),
collected_all_disease_terms
)
)gwas_study_info |>
filter(grepl(vec_to_grep_pattern("hypersensitivity reaction disease"),
collected_all_disease_terms,
perl = T)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Nevirapine-induced hypersensitivity in HIV"gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("hypersensitivity reaction disease")))gwas_study_info |>
filter(grepl(vec_to_grep_pattern("inflammatory skin disease"),
collected_all_disease_terms,
perl = T)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Inflammatory skin disease"gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("inflammatory skin disease"),
replacement = "atopic dermatitis, psoriasis"
)
)gwas_study_info |>
filter(grepl("autosomal dominant compelling helio-ophthalmic outburst syndrome", collected_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Photic sneeze reflex"# remove autosomal dominant compelling helio-ophthalmic outburst syndrome
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = "autosomal dominant compelling helio-ophthalmic outburst syndrome"
))gwas_study_info |>
filter(grepl("skin sensitivity to sun", collected_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique() [1] "Skin sensitivity to sun"
[2] "Ease of sunburn"
[3] "Ease of skin tanning"
[4] "Ease of skin tanning - Get mildly or occasionally tanned (UKB data field 1727)"
[5] "Ease of skin tanning - Get moderately tanned (UKB data field 1727)"
[6] "Ease of skin tanning - Get very tanned (UKB data field 1727)"
[7] "Ease of skin tanning - Never tan only burn (UKB data field 1727)"
[8] "Ease of skin tanning - Get mildly or occasionally tanned (UKB data field 1727) (Gene-based burden)"
[9] "Ease of skin tanning - Get moderately tanned (UKB data field 1727) (Gene-based burden)"
[10] "Ease of skin tanning - Never tan only burn (UKB data field 1727) (Gene-based burden)"
[11] "Ease of skin tanning - Get very tanned (UKB data field 1727) (Gene-based burden)" # remove skin sensitivity to sun
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("skin sensitivity to sun")
))
# also remove suntan
gwas_study_info |>
filter(grepl("suntan", collected_all_disease_terms)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Tanning" "Low tan response"gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("suntan"
)
))# if DISEASE/TRAIT contains Unidentified bright object on brain MRI,
# then replace abnormal brain morphology with Other abnormal findings on diagnostic imaging of central nervous system
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Unidentified bright object on brain MRI",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormal brain morphology"),
"other abnormal findings on diagnostic imaging of central nervous system"
),
collected_all_disease_terms
)
)gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Disorders of lipid metabolism",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormal circulating lipid concentration"),
"disorders of lipid metabolism"
),
collected_all_disease_terms
)
)# if abnormal ecg in disease/trait, then change abnormal ekg to abnormal ecg
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("abnormal ecg",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormal ekg"),
"abnormal ecg"
),
collected_all_disease_terms
)
)gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"gait imbalance",
"decreased walking ability",
"postural instability")
),
"abnormality of gait"
))gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"abnormality of the musculature, abnormality of the nervous system, abnormality of the skeletal system")
),
"other symptoms and signs involving the nervous and musculoskeletal systems"
))# if DISEASE/TRAIT contains PheCode 341
# replace abnormality of the nervous system, with other demyelinating diseases of central nervous system
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("PheCode 341",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormality of the nervous system"),
"other demyelinating diseases of central nervous system"
),
collected_all_disease_terms
)
)
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("PheCode 345",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormality of the nervous system"),
"epilepsy"
),
collected_all_disease_terms
)
)
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Neurological involvement in Behcet's disease",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_remove_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormality of the nervous system")
),
collected_all_disease_terms
)
)gwas_study_info |>
filter(grepl(vec_to_grep_pattern("abdominal abscess"),
collected_all_disease_terms, perl = T)) DISEASE/TRAIT PUBMED_ID YEAR
<char> <int> <int>
1: Abdominal infection 35173190 2022
STUDY
<char>
1: A genome-wide association study in a large community-based cohort identifies multiple loci associated with susceptibility to bacterial and viral infections.
STUDY_ACCESSION MAPPED_TRAIT MAPPED_TRAIT_URI
<char> <char> <char>
1: GCST90103953 abdominal abscess http://www.ebi.ac.uk/efo/EFO_1001753
MAPPED_BACKGROUND_TRAIT MAPPED_BACKGROUND_TRAIT_URI disease_terms
<char> <char> <char>
1: abdominal abscess
MAPPED_TRAIT_CATEGORY background_disease_terms BACKGROUND_TRAIT_CATEGORY
<char> <char> <char>
1: Disease/Disorder Other
DISEASE_STUDY all_disease_terms collected_all_disease_terms
<lgcl> <char> <char>
1: TRUE abdominal abscess abdominal abscess# just one study - 35173190, has abdominal abscess
# they define unusually as: D73.3, K35-37, K57, K61, K63.0, K65, K75.0, K81, K83.0
# 'Abdominal infections'
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == "35173190",
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abdominal abscess"),
"abdominal infections code"
),
collected_all_disease_terms
)
)# if DISEASE/TRAIT contains Abnormal mammogram, then change Abnormality of the breast to abnormal mammogram
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Abnormal findings on mammogram or breast exam",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormality of the breast"),
"abnormal mammogram"
),
collected_all_disease_terms
)
)gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("achalasia"),
"achalasia of cardia"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("asparaginase-induced acute pancreatitis"),
"acute pancreatitis"
))# If `DISEASE/TRAIT` contains Diarrhoea-associated Entamoeba histolytica infection
# then replace amebiasis with amoeboma of intestine
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Diarrhoea-associated Entamoeba histolytica infection",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("amebiasis"),
"amoeboma of intestine"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("chronic mountain sickness"),
"altitude sickness"
))alopecia_terms <- c("frontal fibrosing alopecia"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(alopecia_terms),
"alopecia"
)
)
drug_induced_alopecia_terms <- c(
"chemotherapy-induced alopecia"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(drug_induced_alopecia_terms),
"drug-induced androgenic alopecia"
)
)# alcohol and nicotine codependence -> alcohol dependence, nicotine dependence
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("alcohol and nicotine codependence"),
"alcohol dependence, nicotine dependence"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("alcohol dependence"),
"alcohol-related disorders"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("nicotine dependence"),
"tobacco use disorder"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("al amyloidosis"),
"amyloidosis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("anxiety"),
"anxiety disorder"
)) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("severe aplastic anemia"),
"aplastic anemia"
))gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("androgenetic alopecia"),
"androgenic alopecia"
)) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("angioedema"),
"angioneurotic oedema"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("corneal astigmatism"),
"astigmatism"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("atopic asthma", "chronic obstructive asthma")),
"asthma"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("childhood onset asthma",
"adult onset asthma",
"aspirin-induced asthma"
)
),
"asthma"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("atrial flutter"),
"atrial fibrillation and flutter"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("recalcitrant atopic dermatitis"),
"atopic dermatitis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("macular telangiectasia type 2"
)
),
"background retinopathy and retinal vascular changes"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"bacterial infection"
)
),
"bacterial infection nos"
))# if `DISEASE/TRAIT contains Benign mammary dysplasia`, then change abnormality of the breast to benign mammary dysplasia
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Benign mammary dysplasia",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormality of the breast"),
"benign mammary dysplasia"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("bipolar ii disorder",
"bipolar i disorder"
)
),
"bipolar disorder"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"bronchopneumonia, lung abscess"
)
),
"bronchopneumonia and lung abscess"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"blindness",
"progressive visual loss",
"visual loss"
)
),
"blindness and low vision"
))
# Disorders of optic nerve and visual pathways
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"visual pathway disorder",
"optic nerve disorder"
)
),
"disorders of optic nerve and visual pathways"
))
# visuospatial impairment
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"visuospatial impairment"
)
),
"other and unspecified symptoms and signs involving cognitive functions and awareness"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("cafe-au-lait spot"),
"café au lait spots"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"ocular melanoma")
),
"cancer of eye"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"vaginal yeast infection")
),
"candidiasis of vulva and vagina"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"carbuncle", "furuncle")
),
"carbuncle and furuncle"
))arrhythmia_terms <-
c("ventricular arrhythmia",
"torsades de pointes"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(arrhythmia_terms),
"cardiac arrhythmia"
))cardiomyopathy_terms <- c("nonischemic cardiomyopathy")
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(cardiomyopathy_terms),
"cardiomyopathy"
)
)gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("refractory celiac disease"),
"celiac disease"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("central nervous system origin vertigo"),
"central origin vertigo"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("peripheral vertigo"),
"peripheral or central vertigo"
))# if Brain vascular atherosclerosis in DISEASE/TRAIT, then change vascular brain injury to cerebral atherosclerosis
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Brain vascular atherosclerosis",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("vascular brain injury"),
"cerebral atherosclerosis"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Vascular brain injury",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"vascular brain injury"
)
),
"cerebrovascular disease"
),
collected_all_disease_terms)
)# anorectal malformation to congenital anomalies of intestine
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("anorectal malformation"),
"congenital anomalies of intestine"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Ischemic stroke \\(cardioembolic\\)",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"cardiac embolism"
)),
"cardioembolic stroke"
),
collected_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"mri defined brain infarct",
"cardioembolic stroke")
),
"cerebral infarction"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("cervical cancer, dysplasia"),
"cervical cancer, cervical dysplasia"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"22q11.2 deletion syndrome",
"abnormality of chromosome segregation",
"fragile x syndrome")
),
"chromosomal anomalies"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("sclerosing cholangitis"),
"cholangitis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("stage 5 chronic kidney disease"),
"chronic kidney disease"
))# if Non-alcoholic chronic pancreatitis in `DISEASE/TRAIT`,
# then non-alcoholic pancreatitis to chronic pancreatitis
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Non-alcoholic chronic pancreatitis",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("non-alcoholic pancreatitis"),
"chronic pancreatitis"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"chronic widespread pain",
"multisite chronic pain",
"chronic musculoskeletal pain",
"chronic pain syndrome")
),
"chronic pain"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("chronic pharyngitis, nasopharyngitis")
),
"chronic pharyngitis, chronic nasopharyngitis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("chronic rhinosinusitis with nasal polyps"),
"chronic rhinosinusitis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("chronic sinus infection"),
"chronic sinusitis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("perianal crohns disease"),
"crohns disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("cluster headache"),
"cluster headache syndrome"
))brain_atropy <- c("frontotemporal dementia",
"grn-related frontotemporal lobar degeneration with tdp43 inclusions",
"pick disease")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(brain_atropy),
"circumscribed brain atrophy"
))pattern <- vec_to_grep_pattern("contact dermatitis due to nickel")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = pattern,
"contact dermatitis"
))congenital_heart_disease_terms <- c(
"heart septal defect",
"atrial heart septal defect",
"congenital left-sided heart lesions",
"congenital right-sided heart lesions",
"congenital anomaly of the great arteries", # equiv = "Congenital malformation of great arteries, unspecified"
# malformation of cardiac septum,
"abnormal cardiac septum morphology",
"atrioventricular canal defect",
"ventricular outflow obstruction"
)
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0005207/descendants"
congenital_heart_disease_terms <- c(congenital_heart_disease_terms,
get_descendants(url)
) |>
unique()[1] "Number of terms collected:"
[1] 106
[1] "\n Some example terms"
[1] "double outlet right ventricle with subaortic or doubly committed ventricular septal defect with pulmonary stenosis"
[2] "gata6-related congenital heart disease with or without pancreatic agenesis or neonatal diabetes"
[3] "double outlet right ventricle with non-committed subpulmonary ventricular septal defect"
[4] "congenitally uncorrected transposition of the great arteries with cardiac malformation"
[5] "congenitally uncorrected transposition of the great arteries with coarctation" gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(congenital_heart_disease_terms),
"congenital heart disease"
)
)
# if DISEASE/TRAIT contains Congenital heart disease
# then replace abnormal cardiovascular system morphology with congenital heart disease
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Congenital heart disease",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("abnormal cardiovascular system morphology"),
"congenital heart disease"
),
collected_all_disease_terms
)
)
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0024239/descendants"
more_congenital_heart_disease_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 230
[1] "\n Some example terms"
[1] "double outlet right ventricle with subaortic or doubly committed ventricular septal defect with pulmonary stenosis"
[2] "double outlet right ventricle with atrioventricular septal defect, pulmonary stenosis, heterotaxy"
[3] "gata6-related congenital heart disease with or without pancreatic agenesis or neonatal diabetes"
[4] "double outlet right ventricle with subaortic or doubly committed ventricular septal defect"
[5] "pulmonary valve agenesis-ventricular septal defect-persistent ductus arteriosus syndrome" congenital_heart_disease_terms <- c(congenital_heart_disease_terms,
more_congenital_heart_disease_terms
) |>
unique() |>
str_length_sort()
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(congenital_heart_disease_terms),
"congenital anomaly of cardiovascular system"
)
)cardiac_congenital_anomalies_terms <- c(
"bicuspid aortic valve"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(cardiac_congenital_anomalies_terms),
"cardiac congenital anomalies"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("infantile hypertrophic pyloric stenosis"),
"congenital hypertrophic pyloric stenosis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("congenital hypothyroidism due to developmental anomaly"),
"congenital hypothyroidism"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"diastolic heart failure",
"systolic heart failure")
),
"congestive heart failure \\(chf\\) nos"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"coronary aneurysm",
"coronary artery dissection")
),
"coronary artery aneurysm and dissection"
))
# Aortic aneurysm
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"thoracic aortic aneurysm")
),
"aortic aneurysm"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("sporadic creutzfeld jacob disease",
"creutzfeldt jacob disease",
"creutzfeldt-jacob disease")
),
"creutzfeldt-jakob disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("cryoglobulinemia"),
"cryoglobulinaemia"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("cystic fibrosis associated meconium ileus"),
"cystic fibrosis with intestinal manifestations"
))macular <- c("macular degeneration",
"atrophic macular degeneration",
"retinal drusen"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(macular),
"degeneration of macula and posterior pole"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("clinically amyopathic dermatomyositis"),
"dermatomyositis"
))dental_caries_terms <- c("pit and fissure surface dental caries",
"smooth surface dental caries",
"primary dental caries",
"enamel caries",
"permanent dental caries"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(dental_caries_terms),
"dental caries"
)
)depress_epi <- c("depressive",
"depression",
"depressive disorder"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(depress_epi),
"depressive episode"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(depress_epi),
"depressive episode"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("idiopathic dilated cardiomyopathy"),
"dilated cardiomyopathy"
))terms <- c("ageusia",
"abnormality of the sense of smell")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(terms),
"disturbances of sensation of smell and taste"
)
)tooth_dev_terms <- c("dental enamel hypoplasia",
"tooth agenesis",
"molar-incisor hypomineralization"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(tooth_dev_terms),
"disorders of tooth development"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("hyperuricemia"),
"disorders of purine and pyrimidine metabolism"
))refractive_terms <- c("hyperopia",
"refractive error"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(refractive_terms),
"disorders of refraction and accommodation"
)
)wbc_terms <- c("leukopenia")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(wbc_terms),
"diseases of white blood cells"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("amino acid metabolism disease"),
"disorders of amino-acid metabolism"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("beta-lactam allergy"),
"drug allergy"
))# if DISEASE/STUDY contains eczema, change eczematoid dermatitis to eczema
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("eczema",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("eczematoid dermatitis"),
"eczema"
),
collected_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("hand eczema"),
"eczema"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c(
"early onset hypertension",
"treatment-resistant hypertension")),
"essential hypertension"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("bladder exstrophy"),
"exstrophy of urinary bladder"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"mmr-related febrile seizures",
"febrile seizure")
),
"febrile convulsions"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("peanut allergy",
"milk allergy",
"egg allergy",
"wheat allergic reaction"
)),
"food allergy"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("fuchs endothelial dystrophy"),
"fuchs endothelial corneal dystrophy"
))ginival_and_periodontal_terms <- c("periodontal pocket",
"periodontal disorder",
"gingival disease",
"gingival bleeding"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(ginival_and_periodontal_terms),
"gingival and periodontal diseases"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0005041/descendants"
glaucoma_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 19
[1] "\n Some example terms"
[1] "cyp1b1-related glaucoma with or without anterior segment dysgenesis"
[2] "glaucoma secondary to spherophakia/ectopia lentis and megalocornea"
[3] "hereditary glaucoma, primary closed-angle"
[4] "primary angle closure glaucoma"
[5] "secondary dysgenetic glaucoma" gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(glaucoma_terms),
"glaucoma"
))graft_vs_host_terms <- c("chronic graft versus host disease",
"chronic graft vs. host disease",
"acute graft versus host disease",
"acute graft vs. host disease"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(graft_vs_host_terms),
"graft versus host disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("age-related hearing impairment"),
"presbycusis"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"deafness",
"noise-induced hearing loss")
),
"hearing loss"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("hemiparesis")),
"hemiplegia"
))# if DISEASE/TRAIT contains hepatic steatosis in non-alcoholic fatty liver disease
# replace hepatic steatosis with nonalcoholic steatohepatitis
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("hepatic steatosis in non-alcoholic fatty liver disease",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("hepatic steatosis"),
"nonalcoholic steatohepatitis"
),
collected_all_disease_terms
)
)
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("non-alcoholic steatohepatitis"),
"nonalcoholic steatohepatitis"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("hereditary hemochromatosis type 1"),
"hereditary hemochromatosis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("hordeolum"),
"hordeolum and other deep inflammation of eyelid"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"familial hypercholesterolemia"
)),
"hypercholesterolemia"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"familial hyperlipidemia"
)),
"hyperlipidemia"
))gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c(
"aids dementia",
"hiv-associated neurocognitive disorder")
),
"hiv disease resulting in encephalopathy"
))# "arterial stenosis" -> "Intracranial artery stenosis"
# where DISEASE/TRAIT contains "Intracranial artery stenosis"
# replace "arterial stenosis" with "intracranial artery stenosis"
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Intracranial artery stenosis",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
pattern = "arterial stenosis",
replacement = "intracranial artery stenosis"
),
collected_all_disease_terms
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0019118/descendants"
inherited_retinal_dystrophy_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 349
[1] "\n Some example terms"
[1] "spondyloepiphyseal dysplasia, sensorineural hearing loss, impaired intellectual development, and leber congenital amaurosis"
[2] "x-linked intellectual disability-limb spasticity-retinal dystrophy-diabetes insipidus syndrome"
[3] "microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability"
[4] "retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations"
[5] "retinal dystrophy with inner retinal dysfunction and ganglion cell anomalies" gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(inherited_retinal_dystrophy_terms),
"hereditary retinal dystrophy"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("self-injurious behavior",
"self-injurious ideation")),
"intentional self-harm by unspecified means"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("azoospermia",
"sertoli cell-only syndrome")
),
"male infertility"
) )gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("peyronie disease")
),
"induratio penis plastica"
) )gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("non-lobar intracerebral hemorrhage",
"lobar intracerebral hemorrhage")
),
"intracerebral hemorrhage"
) )url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F36803009/descendants"
idiopathic_generalized_epilepsy_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 4
[1] "\n Some example terms"
[1] "epilepsy with generalized tonic-clonic seizures alone (disorder)"
[2] "juvenile myoclonic epilepsy"
[3] "childhood absence epilepsy"
[4] "juvenile absence epilepsy"
[5] NA idiopathic_generalized_epilepsy_terms = stringr::str_remove_all(
idiopathic_generalized_epilepsy_terms,
" \\(disorder\\)$"
)
idiopathic_generalized_epilepsy_terms = c("epilepsy with generalized tonic-clonic seizures",
idiopathic_generalized_epilepsy_terms
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(idiopathic_generalized_epilepsy_terms),
"generalized idiopathic epilepsy and epileptic syndromes"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("autoimmune thrombocytopenic purpura"),
"idiopathic thrombocytopenic purpura"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("rheumatoid factor-negative juvenile idiopathic arthritis"),
"juvenile idiopathic arthritis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("keratoconjunctivitis sicca"),
"keratoconjunctivitis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("dyslexia",
"mathematics disorder",
"disorder of written expression"
)
),
"learning disorder"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("lewy body attribute"),
"lewy body dementia"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("migraine with aura",
"migraine without aura",
"migraine disorder"
)
),
"migraine"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("relapsing-remitting multiple sclerosis"),
"multiple sclerosis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("late-onset myasthenia gravis"),
"myasthenia gravis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("narcolepsy-cataplexy syndrome"),
"narcolepsy and cataplexy"
))nephro_terms <- c("uric acid nephrolithiasis",
"calcium phosphate nephrolithiasis",
"calcium oxalate nephrolithiasis",
"struvite nephrolithiasis")
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(nephro_terms),
"nephrolithiasis"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("acute tubulointerstitial nephritis",
"iga glomerulonephritis",
"membranous glomerulonephritis",
"lupus nephritis")
),
"nephritis and nephropathy with pathological lesion"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("neurofibromatosis type 1",
"neurofibromatosis type 2")
),
"neurofibromatosis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("aquaporin-4 antibody positive neuromyelitis optica",
"aquaporin-4 antibody negative neuromyelitis optica",
"aqp4-igg-positive neuromyelitis optica",
"aqp4-igg-negative neuromyelitis optica"
)
),
"neuromyelitis optica"
))non_inflam_terms <- c("abnormal vaginal discharge itching",
"abnormal vaginal discharge smell",
"vaginal discharge")
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern =
vec_to_grep_pattern(
non_inflam_terms
),
"noninflammatory disorders of vagina"
)
)gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern =
vec_to_grep_pattern(
c("morbid obesity",
"metabolically healthy obesity"
)
),
"obesity"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c
("obsessive-compulsive trait",
"obsessive-compulsive")
),
"obsessive-compulsive disorder"
))# if Brain vascular stenosis in DISEASE/TRAIT, then change vascular brain injury to occlusion of cerebral arteries
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Brain vascular stenosis",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("vascular brain injury"),
"occlusion of cerebral arteries"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("heroin dependence",
"opioid use disorder")),
"opioid dependence"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("idiopathic osteonecrosis of the femoral head"),
"osteonecrosis"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("osteoradionecrosis"),
"osteonecrosis"
))gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("mesial temporal lobe epilepsy with hippocampal sclerosis",
"rolandic epilepsy")
),
"epilepsy"
)) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("hepatitis c induced liver cirrhosis",
"biliary liver cirrhosis")
),
"other and unspecified cirrhosis of liver"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("familial long qt syndrome")
),
"other cardiac conduction disorders"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("brain atrophy",
"hippocampal atrophy"
)
),
"other cerebral degenerations"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("non-alcoholic fatty liver disease"
)),
"other chronic nonalcoholic liver disease"
))other_bone_cartilage_terms <- c("tietze syndrome"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(other_bone_cartilage_terms),
"other disorders of bone and cartilage"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("dermatochalasis",
"filarial elephantiasis"
)
),
"other disorders of eyelids"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("iris disorder"
)
),
"other disorders of iris and ciliary body"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("binge eating")
),
"other eating disorders"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("hemoglobin e disease"),
"other haemoglobinopathies"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("paraplegia",
"quadriplegia")
),
"other paralytic syndromes"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("corticobasal degeneration disorder"
)
),
"other specified degenerative diseases of nervous system"
))
# progressive supranuclear palsy -> Dementia with cerebral degenerations
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("progressive supranuclear palsy"),
"dementia with cerebral degenerations"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("primary biliary cholangitis",
"primary sclerosing cholangitis"
)
),
"non-alcoholic steatohepatitis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("retinal edema"
)),
"other specified retinal disorders"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("young adult-onset parkinsonism"),
"parkinsons disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("neonatal jaundice"),
"perinatal jaundice"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("aggressive periodontitis"),
"periodontitis"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("thrombophlebitis")),
"phlebitis and thrombophlebitis"
))# social anxiety disorder -> social phobias
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("social anxiety disorder"),
"social phobias"
))
# specific phobia -> Specific \\(isolated\\) phobias
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("specific phobia"),
"specific \\(isolated\\) phobias"
))# where Pigmentary iris degeneration in DISEASE/TRAIT & pubmed id 39024449
# replace abnormality of the eye with pigmentary iris degeneration
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Pigmentary iris degeneration",
`DISEASE/TRAIT`,
ignore.case = TRUE) & PUBMED_ID == "39024449",
stringr::str_replace_all(collected_all_disease_terms,
pattern = "abnormality of the eye",
replacement = "pigmentary iris degeneration"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("central precocious puberty"),
"precocious puberty"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("premature menopause"),
"premature menopause and other ovarian failure"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("primary aldosteronism"),
"primary hyperaldosteronism"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("primary ovarian insufficiency"),
"primary ovarian failure"
))# if DISEASE/TRAIT contains PheCode 286.8
# then replce thrombophilia with primary thrombophilia
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("PheCode 286.8",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("thrombophilia"),
"primary thrombophilia"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("albuminuria",
"moderate albuminuria")
),
"proteinuria"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("prurigo"),
"other prurigo"
))psoriasis_terms <- c("cutaneous psoriasis")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(psoriasis_terms),
"psoriasis")
)psychosis_terms <- c("psychotic",
"psychotic symptoms"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(psychosis_terms),
"psychosis")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("idiopathic pulmonary fibrosis"),
"pulmonary fibrosis"
))# for pubmed id: 37469131
# and DISEASE/TRAIT contains 'rush' (a tyop of rash)
# replace purpura with rash, petechiae
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == 37469131 & grepl("rush", `DISEASE/TRAIT`, ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("purpura"),
"rash, petechiae"
),
collected_all_disease_terms
)
)rash_terms <- c(
"maculopapular eruption"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(rash_terms),
"rash and other nonspecific skin eruption"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("retinoschisis"),
"retinoschisis and retinal cysts"
))ra_terms <- c("acpa-positive rheumatoid arthritis",
"acpa-negative rheumatoid arthritis",
"adult-onset stills disease")
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(ra_terms),
"rheumatoid arthritis"
)
)rhinitis_terms <- c("non-allergic rhinitis")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(rhinitis_terms),
"rhinitis"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("ldh-related sciatica")
),
"sciatica"
)) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("schizoaffective disorder-bipolar type"),
"schizoaffective disorder")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("treatment refractory schizophrenia"),
"schizophrenia")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("adolescent idiopathic scoliosis"),
"scoliosis")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("central serous retinopathy",
"chronic central serous retinopathy")
),
"separation of retinal layers"
))sleep_apnea_terms <- c("sleep apnea during non-rem sleep",
"sleep apnea during rem sleep",
"obstructive sleep apnea")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(sleep_apnea_terms),
"sleep apnea")
)sleep_disorder_terms <- c("sleepiness",
"somnambulism",
"rem sleep behavior disorder",
"periodic limb movement disorder",
"bruxism"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(sleep_disorder_terms),
"sleep disorders"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("specific language impairment",
"language impairment",
"social communication impairment"
)
),
"speech and language disorder"
))
# if DISEASE/TRAIT contains Developmental stuttering
# then replace stuttering with speech and language disorder
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Developmental stuttering",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("stuttering"),
"speech and language disorder"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("staphylococcus aureus infection",
"skin and soft tissue staphylococcus aureus infection",
"methicillin-resistant staphylococcus aureus infection")),
"staphylococcus infections"
))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_540/descendants"
strabismus_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 26
[1] "\n Some example terms"
[1] "abnormal retinal correspondence" "brown's tendon sheath syndrome"
[3] "internuclear ophthalmoplegia" "duane retraction syndrome 3"
[5] "duane retraction syndrome 2" strabismus_terms = c("non-accomodative esotropia",
strabismus_terms)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(strabismus_terms),
"strabismus"
))other_nonspec_stroke <- c("large artery stroke",
"small vessel stroke",
"stroke outcome",
"stroke disorder"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(other_nonspec_stroke),
"stroke"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("PheCode 313.2",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("stuttering, tics")),
"tics and stuttering"
),
collected_all_disease_terms
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("PheCode 333.3",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(c("stuttering, tics")),
"tics and choreas"
),
collected_all_disease_terms
))terms <- c("diffuse scleroderma",
"limited scleroderma",
"anti-centromere-antibody-positive systemic scleroderma",
"anti-topoisomerase-i-antibody-positive systemic scleroderma")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(terms),
"systemic sclerosis"
))# if DISEASE/TRAIT contains Ringworm, replace tinea with tinea corporis
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Ringworm",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("tinea"),
"tinea corporis"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("hyperthyroidism"),
"thyrotoxicosis with or without goiter"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
"^treatment-resistant |^treatment resistant |^treatment-resistant "
))# if DISEASE/TRAIT contains Treatment resistant depression
# then replace depression with treatment resistant depression
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Treatment resistant depression",
`DISEASE/TRAIT`,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("depression"),
"treatment resistant depression"
),
collected_all_disease_terms
)
)
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("treatment resistant depression",
MAPPED_BACKGROUND_TRAIT,
ignore.case = TRUE),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("depression"),
"treatment resistant depression"
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("latent autoimmune diabetes in adults"),
"type 1 diabetes mellitus"
))icd_terms <- c("type 1 diabetes with foot ulcer",
"type 2 diabetes with foot ulcer",
"type 1 diabetes with diabetic neuropathy",
"type 2 diabetes with diabetic neuropathy")
icd_replacement <- paste0(icd_terms, collapse = ", ")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("diabetic foot, neuropathy, type 1 diabetes mellitus, type 2 diabetes mellitus"),
icd_replacement
))type_2_eye_terms <- c("diabetes mellitus type 2 associated cataract",
"diabetic maculopathy, type 2 diabetes mellitus",
"diabetic macular edema, type 2 diabetes mellitus",
"proliferative diabetic retinopathy, type 2 diabetes mellitus",
"macrovascular complications of diabetes, type 2 diabetes mellitus"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(type_2_eye_terms),
"type 2 diabetes with ophthalmic manifestations"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(type_2_eye_terms),
"type 2 diabetes with ophthalmic manifestations"
))
# for 30487263, all discovery samples are type 2 diabetes - so
# replace proliferative diabetic retinopathy with type 2 diabetes with ophthalmic manifestations
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == 30487263,
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("proliferative diabetic retinopathy"),
"type 2 diabetes with ophthalmic manifestations"
),
collected_all_disease_terms
)
)
# for pubmed id: 31482010
# all samples are type 2 diabetes
# so replace diabetic retinopathy with type 2 diabetes with ophthalmic manifestations
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(PUBMED_ID == 31482010,
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("proliferative diabetic retinopathy"),
"type 2 diabetes with ophthalmic manifestations"
),
collected_all_disease_terms
)
)
# neuropathic pain, type 2 diabetes mellitus
# change to type 2 diabetes with diabetic neuropathy
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("neuropathic pain, type 2 diabetes mellitus"),
"type 2 diabetes with ophthalmic manifestations"
)
)gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("Menstruation",
`DISEASE/TRAIT`,
ignore.case = TRUE),
str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("decreased attention"),
"unspecified condition associated with female genital organs and menstrual cycle"),
collected_all_disease_terms
)
)uveitis_terms <- c("anterior uveitis",
"iritis",
"vogt-koyanagi-harada disease",
"birdshot chorioretinopathy",
"multifocal choroiditis"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(uveitis_terms),
"uveitis"
))gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("anti-neutrophil antibody associated vasculitis"),
"vasculitis"
)
)diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms[gwas_study_info$collected_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
diseases <- unique(diseases)
print(length(diseases))[1] 1963fwrite(
gwas_study_info,
here::here("output/gwas_cat/gwas_study_all_group.csv")
)
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] jsonlite_2.0.0 httr_1.4.7 data.table_1.17.8 stringr_1.6.0
[5] dplyr_1.1.4 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] compiler_4.3.1 BiocManager_1.30.26 renv_1.0.3
[4] promises_1.3.3 tidyselect_1.2.1 Rcpp_1.1.0
[7] git2r_0.36.2 callr_3.7.6 later_1.4.4
[10] jquerylib_0.1.4 yaml_2.3.10 fastmap_1.2.0
[13] here_1.0.1 R6_2.6.1 generics_0.1.4
[16] curl_7.0.0 knitr_1.50 tibble_3.3.0
[19] rprojroot_2.1.0 bslib_0.9.0 pillar_1.11.1
[22] rlang_1.1.6 cachem_1.1.0 stringi_1.8.7
[25] httpuv_1.6.16 xfun_0.55 getPass_0.2-4
[28] fs_1.6.6 sass_0.4.10 cli_3.6.5
[31] withr_3.0.2 magrittr_2.0.4 ps_1.9.1
[34] digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1
[37] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.5
[40] glue_1.8.0 whisker_0.4.1 rmarkdown_2.30
[43] tools_4.3.1 pkgconfig_2.0.3 htmltools_0.5.8.1