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| Rmd | 9c64867 | IJbeasley | 2025-09-09 | Minor fixing of disease trait categorisation |
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library(dplyr)
library(data.table)
library(ggplot2)
library(stringr)source(here::here("code/get_term_descendants.R"))gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_group_l1_v2.csv"))gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms = l1_all_disease_terms)gwas_study_info |>
filter(grepl("lip and oral cavity cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: oral cavity cancer
2: mouth neoplasm
3: tongue cancer
4: major salivary gland cancer
5: human papilloma virus infection, oral cavity cancer
6: tongue neoplasm
l2_all_disease_terms
<char>
1: lip and oral cavity cancer
2: lip and oral cavity cancer
3: lip and oral cavity cancer
4: lip and oral cavity cancer
5: human papilloma virus infection, lip and oral cavity cancer
6: lip and oral cavity cancergwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "nasopharyngeal cancer",
"nasopharynx cancer"
)
)
gwas_study_info |>
filter(grepl("nasopharynx cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() all_disease_terms l2_all_disease_terms
<char> <char>
1: nasopharyngeal neoplasm nasopharynx cancergwas_study_info |>
filter(grepl("other pharynx cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: oropharynx cancer
2: laryngeal squamous cell carcinoma, hypopharynx cancer
3: human papilloma virus infection, oropharynx cancer
4: tonsil cancer
5: hypopharyngeal carcinoma
6: pharynx cancer, laryngeal carcinoma
l2_all_disease_terms
<char>
1: other pharynx cancer
2: larynx cancer, other pharynx cancer
3: human papilloma virus infection, other pharynx cancer
4: other pharynx cancer
5: other pharynx cancer
6: larynx cancer, other pharynx cancergwas_study_info |>
filter(grepl("esophageal cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: esophageal adenocarcinoma, barretts esophagus
2: esophageal adenocarcinoma
3: esophageal adenocarcinoma, gastroesophageal reflux disease
4: esophageal squamous cell carcinoma
5: esophageal carcinoma, gastric carcinoma
6: squamous cell carcinoma, esophageal carcinoma
l2_all_disease_terms
<char>
1: barretts esophagus, esophageal cancer
2: esophageal cancer
3: esophageal cancer, gastroesophageal reflux disease
4: esophageal cancer
5: esophageal cancer, stomach cancer
6: esophageal cancergwas_study_info |>
filter(grepl("stomach cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: gastric carcinoma
2: esophageal carcinoma, gastric carcinoma
3: gastric cardia carcinoma
4: gastric adenocarcinoma
5: lung carcinoma, squamous cell carcinoma, gastric carcinoma
6: gastric cancer
l2_all_disease_terms
<char>
1: stomach cancer
2: esophageal cancer, stomach cancer
3: stomach cancer
4: stomach cancer
5: lung cancer, stomach cancer
6: stomach cancergwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "colorectal cancer",
"colon and rectum cancer"
)
)
gwas_study_info |>
filter(grepl("colon and rectum cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: colorectal cancer
2: sclerosing cholangitis, colorectal cancer
3: colorectal cancer, colorectal adenoma
4: metastatic colorectal cancer
5: lung carcinoma, estrogen-receptor negative breast cancer, ovarian endometrioid carcinoma, colorectal cancer, prostate carcinoma, ovarian serous carcinoma, breast carcinoma, ovarian carcinoma, lung adenocarcinoma, squamous cell lung carcinoma, cancer
6: rectum cancer
l2_all_disease_terms
<char>
1: colon and rectum cancer
2: colon and rectum cancer, sclerosing cholangitis
3: benign neoplasm, colon and rectum cancer
4: colon and rectum cancer
5: breast cancer, cancer, colon and rectum cancer, lung cancer, ovarian cancer, prostate cancer
6: colon and rectum cancergwas_study_info |>
filter(grepl("liver cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: hepatitis b virus infection, hepatocellular carcinoma
2: sclerosing cholangitis, cholangiocarcinoma
3: cholangiocarcinoma, sclerosing cholangitis
4: sclerosing cholangitis, hepatocellular carcinoma
5: hepatitis c virus infection, hepatocellular carcinoma
6: hepatocellular carcinoma, non-alcoholic steatohepatitis
l2_all_disease_terms
<char>
1: hepatitis b infection, liver cancer
2: liver cancer, sclerosing cholangitis
3: liver cancer, sclerosing cholangitis
4: liver cancer, sclerosing cholangitis
5: hepatitis c infection, liver cancer
6: liver cancer, non-alcoholic fatty liver diseasegwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
case_when(
l2_all_disease_terms == "cancer of gallbladder and extrahepatic biliary tract" ~ "gallbladder and biliary tract cancer",
TRUE ~ l2_all_disease_terms
)
)
gwas_study_info |>
filter(grepl("gallbladder and biliary tract cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() all_disease_terms
<char>
1: sclerosing cholangitis, gallbladder neoplasm
2: gallbladder neoplasm
l2_all_disease_terms
<char>
1: gallbladder and biliary tract cancer, sclerosing cholangitis
2: gallbladder and biliary tract cancergwas_study_info |>
filter(grepl("pancreatic cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: pancreatic carcinoma
2: pancreatic ductal adenocarcinoma
3: pancreatic carcinoma, neutropenia
4: breast carcinoma, estrogen-receptor positive breast cancer, metastatic prostate cancer, pancreatic carcinoma, hypertension
5: breast carcinoma, estrogen-receptor positive breast cancer, metastatic prostate cancer, pancreatic carcinoma, proteinuria
6: breast carcinoma, estrogen-receptor positive breast cancer, metastatic prostate cancer, pancreatic carcinoma, hypertension, proteinuria
l2_all_disease_terms
<char>
1: pancreatic cancer
2: pancreatic cancer
3: neutropenia, pancreatic cancer
4: breast cancer, hypertension, pancreatic cancer, prostate cancer
5: breast cancer, pancreatic cancer, prostate cancer, proteinuria
6: breast cancer, hypertension, pancreatic cancer, prostate cancer, proteinuriagwas_study_info |>
filter(grepl("larynx cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: laryngeal squamous cell carcinoma
2: laryngeal squamous cell carcinoma, hypopharynx cancer
3: laryngeal carcinoma
4: laryngeal neoplasm
5: glottis neoplasm
6: pharynx cancer, laryngeal carcinoma
l2_all_disease_terms
<char>
1: larynx cancer
2: larynx cancer, other pharynx cancer
3: larynx cancer
4: larynx cancer
5: larynx cancer
6: larynx cancer, other pharynx cancerresp_cancer_terms = c("lung cancer",
"bronchus cancer",
"tracheal cancer",
"respiratory system cancer"
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
ifelse(l2_all_disease_terms != "tracheal bronchus and lung cancer",
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(resp_cancer_terms, collapse = "(?=,|$)|\\b"),
"tracheal bronchus and lung cancer"
),
l2_all_disease_terms
)
)
gwas_study_info |>
filter(grepl("tracheal bronchus and lung cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: non-small cell lung carcinoma
2: lung adenocarcinoma
3: squamous cell lung carcinoma
4: lung carcinoma, family history of lung cancer
5: lung adenocarcinoma, family history of lung cancer
6: squamous cell lung carcinoma, family history of lung cancer
l2_all_disease_terms
<char>
1: tracheal bronchus and lung cancer
2: tracheal bronchus and lung cancer
3: tracheal bronchus and lung cancer
4: tracheal bronchus and lung cancer
5: tracheal bronchus and lung cancer
6: tracheal bronchus and lung cancergwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "malignant melanoma of skin",
"malignant skin melanoma"
)
)
gwas_study_info |>
filter(grepl("malignant skin melanoma", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: cutaneous melanoma
2: melanoma
3: neuroblastoma, cutaneous melanoma
4: skin cancer
5: skin carcinoma
6: melanoma, immune system toxicity
l2_all_disease_terms
<char>
1: malignant skin melanoma
2: malignant skin melanoma
3: malignant skin melanoma, neuroblastoma
4: malignant skin melanoma, non-melanoma skin cancer
5: malignant skin melanoma, non-melanoma skin cancer
6: immune system toxicity, malignant skin melanomagwas_study_info |>
filter(grepl("non-melanoma skin cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() all_disease_terms
<char>
1: squamous cell carcinoma, basal cell carcinoma
2: keratinocyte carcinoma
3: basal cell carcinoma
4: non-melanoma skin carcinoma
5: skin cancer
6: skin neoplasm
7: skin carcinoma in situ
8: skin carcinoma
l2_all_disease_terms
<char>
1: non-melanoma skin cancer
2: non-melanoma skin cancer
3: non-melanoma skin cancer
4: non-melanoma skin cancer
5: malignant skin melanoma, non-melanoma skin cancer
6: non-melanoma skin cancer
7: non-melanoma skin cancer
8: malignant skin melanoma, non-melanoma skin cancergwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "soft tissue sarcoma",
"soft tissue and other extraosseous sarcomas"
)
)
gwas_study_info |>
filter(grepl("soft tissue and other extraosseous sarcomas", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: sarcoma, fibrosarcoma sarcoma, soft tissue and other extraosseous sarcomas
2: kaposis sarcoma soft tissue and other extraosseous sarcomasgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "bone cancer|osteosarcoma",
"malignant neoplasm of bone and articular cartilage"
)
)
gwas_study_info |>
filter(grepl("malignant neoplasm of bone and articular cartilage", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: osteosarcoma
2: acute myeloid leukemia
3: myeloid leukemia
4: malignant bone neoplasm
5: acute myeloid leukemia, myelodysplastic syndrome
6: bone neoplasm
l2_all_disease_terms
<char>
1: malignant neoplasm of bone and articular cartilage
2: malignant neoplasm of bone and articular cartilage
3: malignant neoplasm of bone and articular cartilage
4: malignant neoplasm of bone and articular cartilage
5: malignant neoplasm of bone and articular cartilage, myelodysplastic syndrome
6: malignant neoplasm of bone and articular cartilagegwas_study_info |>
filter(grepl("breast cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: estrogen-receptor negative breast cancer
2: breast carcinoma
3: estrogen-receptor positive breast cancer
4: breast carcinoma,
5: estrogen-receptor positive breast cancer, breast carcinoma
6: estrogen-receptor negative breast cancer, breast carcinoma
l2_all_disease_terms
<char>
1: breast cancer
2: breast cancer
3: breast cancer
4: breast cancer
5: breast cancer
6: breast cancergwas_study_info |>
filter(grepl("cervical cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: cervical carcinoma
2: cervical cancer
3: dysplasia of cervix, cervical cancer
4: dysplasia, cervical cancer
5: uterine cervix carcinoma in situ
6: cervical carcinoma, human papilloma virus infection
l2_all_disease_terms
<char>
1: cervical cancer
2: cervical cancer
3: cervical cancer, dysplasia of cervix
4: cervical cancer, dysplasia
5: cervical cancer
6: cervical cancer, human papilloma virus infection# ? is endometrial cancer a subset of uterine cancer for GBD?
# is for ontology: http://purl.obolibrary.org/obo/MONDO_0002715
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "endometrial cancer",
"uterine cancer"
)
)
gwas_study_info |>
filter(grepl("uterine cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: endometrial endometrioid carcinoma uterine cancer
2: endometrial carcinoma uterine cancer
3: endometrial neoplasm uterine cancer
4: uterine carcinoma uterine cancer
5: endometrial cancer, covid-19 covid-19, uterine cancer
6: uterine corpus cancer uterine cancergwas_study_info |>
filter(grepl("ovarian cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: ovarian carcinoma
2: malignant epithelial tumor of ovary
3: prostate carcinoma, breast carcinoma, ovarian carcinoma
4: lung carcinoma, estrogen-receptor negative breast cancer, ovarian endometrioid carcinoma, colorectal cancer, prostate carcinoma, ovarian serous carcinoma, breast carcinoma, ovarian carcinoma, lung adenocarcinoma, squamous cell lung carcinoma, cancer
5: ovarian mucinous adenocarcinoma
6: ovarian serous carcinoma
l2_all_disease_terms
<char>
1: ovarian cancer
2: ovarian cancer
3: breast cancer, ovarian cancer, prostate cancer
4: breast cancer, cancer, colon and rectum cancer, tracheal bronchus and lung cancer, ovarian cancer, prostate cancer
5: ovarian cancer
6: ovarian cancergwas_study_info |>
filter(grepl("prostate cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: prostate carcinoma
2: cancer aggressiveness measurement, prostate carcinoma
3: prostate carcinoma, breast carcinoma, ovarian carcinoma
4: metastatic prostate cancer, peripheral neuropathy
5: metastatic prostate cancer
6: prostate carcinoma, erectile dysfunction
l2_all_disease_terms
<char>
1: prostate cancer
2: prostate cancer
3: breast cancer, ovarian cancer, prostate cancer
4: peripheral neuropathy, prostate cancer
5: prostate cancer
6: erectile dysfunction, prostate cancergwas_study_info |>
filter(grepl("testicular cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() all_disease_terms
<char>
1: testicular carcinoma
2: testicular carcinoma, cardiovascular disease
3: testicular neoplasm
l2_all_disease_terms
<char>
1: testicular cancer
2: cardiovascular disease, testicular cancer
3: testicular cancergwas_study_info |>
filter(grepl("kidney cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: renal cell carcinoma kidney cancer
2: nephroblastoma kidney cancer
3: kidney cancer kidney cancer
4: clear cell renal carcinoma kidney cancer
5: renal carcinoma kidney cancer
6: papillary renal cell carcinoma kidney cancergwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "urinary bladder cancer",
"bladder cancer"
)
)
gwas_study_info |>
filter(grepl("bladder cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() all_disease_terms
<char>
1: urinary bladder carcinoma
2: urinary bladder carcinoma, disease progression measurement
3: urinary bladder cancer,
4: urinary bladder cancer
l2_all_disease_terms
<char>
1: bladder cancer
2: bladder cancer
3: bladder cancer
4: bladder cancergwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "\\bcentral nervous system cancer\\b",
"brain and central nervous system cancer"
)
)
gwas_study_info |>
filter(grepl("brain and central nervous system cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: glioblastoma multiforme
2: central nervous system cancer
3: glioma
4: central nervous system cancer, glioma
5: central nervous system cancer, glioblastoma multiforme
6: brain neoplasm
l2_all_disease_terms
<char>
1: brain and central nervous system cancer
2: brain and central nervous system cancer
3: brain and central nervous system cancer
4: brain and central nervous system cancer
5: brain and central nervous system cancer
6: brain and central nervous system cancergwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "\\bocular melanoma\\b|ocular cancer\\b",
"eye cancer"
)
)
gwas_study_info |>
filter(grepl("eye cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: uveal melanoma eye cancer
2: choroidal melanoma eye cancer
3: epithelioid cell uveal melanoma eye cancer
4: uveal melanoma, epithelioid cell uveal melanoma eye cancer
5: uveal melanoma disease severity eye cancer
6: ocular cancer eye cancergwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "\\bneuroblastoma\\b|\\bperipheral nervous system cancer\\b",
"neuroblastoma and other peripheral nervous cell tumors"
)
)
gwas_study_info |>
filter(grepl("neuroblastoma and other peripheral nervous cell tumors", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: neuroblastoma
2: neuroblastoma, cutaneous melanoma
l2_all_disease_terms
<char>
1: neuroblastoma and other peripheral nervous cell tumors
2: malignant skin melanoma, neuroblastoma and other peripheral nervous cell tumorsgwas_study_info |>
filter(grepl("thyroid cancer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: differentiated thyroid carcinoma thyroid cancer
2: papillary thyroid carcinoma thyroid cancer
3: follicular thyroid carcinoma thyroid cancer
4: thyroid carcinoma thyroid cancer
5: thyroid cancer thyroid cancergwas_study_info |>
filter(grepl("mesothelioma", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: malignant pleural mesothelioma mesothelioma
2: mesothelioma mesothelioma
3: pleural mesothelioma mesotheliomagwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "hodgkins lymphoma",
"hodgkin lymphoma"
)
)
gwas_study_info |>
filter(grepl("hodgkin lymphoma", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: diffuse large b-cell lymphoma, multiple sclerosis
2: follicular lymphoma, multiple sclerosis
3: marginal zone b-cell lymphoma, multiple sclerosis
4: diffuse large b-cell lymphoma, rheumatoid arthritis
5: rheumatoid arthritis, follicular lymphoma
6: rheumatoid arthritis, marginal zone b-cell lymphoma
l2_all_disease_terms
<char>
1: multiple sclerosis, non-hodgkin lymphoma
2: multiple sclerosis, non-hodgkin lymphoma
3: multiple sclerosis, non-hodgkin lymphoma
4: non-hodgkin lymphoma, rheumatoid arthritis
5: non-hodgkin lymphoma, rheumatoid arthritis
6: non-hodgkin lymphoma, rheumatoid arthritisgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "non-hodgkins lymphoma",
"non-hodgkin lymphoma"
)
)
gwas_study_info |>
filter(grepl("non-hodgkin lymphoma", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: diffuse large b-cell lymphoma, multiple sclerosis
2: follicular lymphoma, multiple sclerosis
3: marginal zone b-cell lymphoma, multiple sclerosis
4: diffuse large b-cell lymphoma, rheumatoid arthritis
5: rheumatoid arthritis, follicular lymphoma
6: rheumatoid arthritis, marginal zone b-cell lymphoma
l2_all_disease_terms
<char>
1: multiple sclerosis, non-hodgkin lymphoma
2: multiple sclerosis, non-hodgkin lymphoma
3: multiple sclerosis, non-hodgkin lymphoma
4: non-hodgkin lymphoma, rheumatoid arthritis
5: non-hodgkin lymphoma, rheumatoid arthritis
6: non-hodgkin lymphoma, rheumatoid arthritisgwas_study_info |>
filter(grepl("multiple myeloma", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: multiple myeloma
2: multiple myeloma, peripheral neuropathy
3: multiple myeloma, chemotherapy-induced oral mucositis
4: multiple myeloma, monoclonal gammopathy
5: hodgkins lymphoma, multiple myeloma, chronic lymphocytic leukemia
6: hodgkins lymphoma, multiple myeloma, non-hodgkins lymphoma
l2_all_disease_terms
<char>
1: multiple myeloma
2: multiple myeloma, peripheral neuropathy
3: chemotherapy-induced oral mucositis, multiple myeloma
4: monoclonal gammopathy, multiple myeloma
5: hodgkin lymphoma, leukemia, multiple myeloma
6: hodgkin lymphoma, multiple myeloma, non-hodgkin lymphomagwas_study_info |>
filter(grepl("leukemia", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: acute lymphoblastic leukemia
2: multiple sclerosis, chronic lymphocytic leukemia
3: rheumatoid arthritis, chronic lymphocytic leukemia
4: systemic lupus erythematosus, chronic lymphocytic leukemia
5: acute lymphoblastic leukemia, asparaginase-induced acute pancreatitis
6: chronic lymphocytic leukemia
l2_all_disease_terms
<char>
1: leukemia
2: leukemia, multiple sclerosis
3: leukemia, rheumatoid arthritis
4: leukemia, systemic lupus erythematosus
5: leukemia, pancreatitis
6: leukemiagwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
case_when(
l2_all_disease_terms == "cancer" ~ "other malignant neoplasms",
TRUE ~ l2_all_disease_terms
)
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
ifelse(PUBMED_ID == 27790247,
stringr::str_replace_all(l2_all_disease_terms,
pattern = ", cancer,",
", other malignant neoplasms,"
),
l2_all_disease_terms
)
)
### dealing with measuring cancer caused factor terms
gwas_study_info |>
filter(grepl("^cancer,", l2_all_disease_terms)) |>
pull(l2_all_disease_terms) |>
unique()[1] "cancer, chronic obstructive pulmonary disease"
[2] "cancer, cardiotoxicity"
[3] "cancer, hand-foot syndrome"
[4] "cancer, peripheral neuropathy"
[5] "cancer, immune system toxicity"
[6] "cancer, hypothyroidism"
[7] "cancer, radiation-induced disorder"
[8] "cancer, osteonecrosis" gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
ifelse(grepl("^cancer,", l2_all_disease_terms),
stringr::str_replace_all(l2_all_disease_terms,
pattern = "^cancer,",
"other malignant neoplasms,"
),
l2_all_disease_terms
)
)
other_malignant_terms <- c(
"retroperitoneal cancer",
"peritoneal cancer",
"ewing sarcoma",
"digestive system cancer",
"intestinal cancer",
"small intestine cancer",
"female reproductive organ cancer",
"male reproductive organ cancer",
"vulvar cancer",
"testicular germ cell tumor",
"urogenital cancer",
"squamous cell cancer",
"head and neck cancer",
"malignant tumor of floor of mouth",
"nasal cavity cancer", #? not sure if should be somewhere else ..
"malignant lymphoid tumor",
"neuroendocrine tumor",
"lymphatic system cancer",
"childhood cancer" #? maybe sort furtrher
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(other_malignant_terms, collapse = "(?=,|$)|\\b"),
"other malignant neoplasms"
)
)
gwas_study_info |>
filter(grepl("other malignant neoplasms", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: squamous cell carcinoma
2: cancer
3: childhood cancer, cardiomyopathy
4: neuroendocrine neoplasm
5: small intestine neuroendocrine tumor
6: pancreatic neuroendocrine tumor
l2_all_disease_terms
<char>
1: other malignant neoplasms
2: other malignant neoplasms
3: cardiomyopathy, other malignant neoplasms
4: other malignant neoplasms
5: other malignant neoplasms
6: other malignant neoplasmsgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
case_when(
l2_all_disease_terms == "benign neoplasm" ~ "other neoplasms",
TRUE ~ l2_all_disease_terms
)
)
unknown_sig_terms <- c("intracranial germ cell tumor",
"bladder tumor")
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(unknown_sig_terms, collapse = "(?=,|$)|\\b"),
"other neoplasms"
)
)
gwas_study_info |>
filter(grepl("other neoplasms", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: benign prostatic hyperplasia other neoplasms
2: colorectal adenoma other neoplasms
3: colorectal cancer, endometrial neoplasm other neoplasms
4: upper aerodigestive tract neoplasm other neoplasms
5: meningioma other neoplasms
6: pituitary gland adenoma other neoplasmsgwas_study_info |>
filter(grepl("rheumatic heart disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: rheumatic heart disease rheumatic heart diseasegwas_study_info |>
filter(grepl("ischemic heart disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: non-obstructive coronary artery disease
2: mucocutaneous lymph node syndrome, coronary aneurysm
3: migraine disorder, coronary artery disease
4: coronary artery disease
5: type 2 diabetes mellitus, obesity, coronary artery disease
6: alzheimer disease, type 2 diabetes mellitus, coronary artery disease
l2_all_disease_terms
<char>
1: ischemic heart disease
2: ischemic heart disease, mucocutaneous lymph node syndrome
3: ischemic heart disease, migraine
4: ischemic heart disease
5: ischemic heart disease, obesity, type 2 diabetes mellitus
6: alzheimers disease, ischemic heart disease, type 2 diabetes mellitus== coronary artery disease (https://www.ncbi.nlm.nih.gov/books/NBK209964/)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "coronary artery disease",
"ischemic heart disease"
)
)gwas_study_info |>
filter(grepl("stroke", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: intracerebral hemorrhage stroke
2: non-lobar intracerebral hemorrhage stroke
3: lobar intracerebral hemorrhage stroke
4: small vessel stroke stroke
5: alzheimer disease, small vessel stroke alzheimers disease, stroke
6: ischemic stroke strokegwas_study_info |>
filter(grepl("hypertensive heart disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: hypertensive heart disease, kidney disease
2: hypertensive heart disease
l2_all_disease_terms
<char>
1: hypertensive heart disease, kidney disease
2: hypertensive heart diseasegwas_study_info |>
filter(grepl("heart valve disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: aortic stenosis, aortic valve calcification heart valve disease
2: aortic stenosis heart valve disease
3: aortic valve calcification heart valve disease
4: mitral valve prolapse heart valve disease
5: aortic valve disease heart valve disease
6: heart valve disease heart valve diseasegwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "heart valve disease",
"non-rheumatic valvular heart disease"
)
)
gwas_study_info |>
filter(grepl("non-rheumatic valvular heart disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: aortic stenosis, aortic valve calcification
2: aortic stenosis
3: aortic valve calcification
4: mitral valve prolapse
5: aortic valve disease
6: heart valve disease
l2_all_disease_terms
<char>
1: non-rheumatic valvular heart disease
2: non-rheumatic valvular heart disease
3: non-rheumatic valvular heart disease
4: non-rheumatic valvular heart disease
5: non-rheumatic valvular heart disease
6: non-rheumatic valvular heart diseasegwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "\\bcardiomyopathy\\b|\\bmyocarditis\\b",
"cardiomyopathy and myocarditis"
)
)
gwas_study_info |>
filter(grepl("cardiomyopathy and myocarditis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: idiopathic dilated cardiomyopathy
2: childhood cancer, cardiomyopathy
3: hypertrophic cardiomyopathy
4: dilated cardiomyopathy
5: chagas cardiomyopathy
6: peripartum cardiomyopathy
l2_all_disease_terms
<char>
1: cardiomyopathy and myocarditis
2: cardiomyopathy and myocarditis, other malignant neoplasms
3: cardiomyopathy and myocarditis
4: cardiomyopathy and myocarditis
5: cardiomyopathy and myocarditis
6: cardiomyopathy and myocarditisgwas_study_info |>
filter(grepl("pulmonary arterial hypertension", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: pulmonary arterial hypertension pulmonary arterial hypertensionafib_terms <- c("atrial fibrillation",
"atrial flutter",
"post-operative atrial fibrillation")
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(afib_terms, collapse = "(?=,|$)|\\b"),
"atrial fibrillation and flutter"
)
)
gwas_study_info |>
filter(grepl("atrial fibrillation and flutter", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: atrial fibrillation
2: heart failure, diabetes mellitus, stroke, atrial fibrillation, coronary artery disease, cancer
3: stroke, atrial fibrillation, coronary artery disease, heart failure, diabetes mellitus, cancer
4: atrial flutter
5: post-operative atrial fibrillation
l2_all_disease_terms
<char>
1: atrial fibrillation and flutter
2: atrial fibrillation and flutter, other malignant neoplasms, diabetes mellitus, heart failure, ischemic heart disease, stroke
3: atrial fibrillation and flutter, other malignant neoplasms, diabetes mellitus, heart failure, ischemic heart disease, stroke
4: atrial fibrillation and flutter
5: atrial fibrillation and flutter, post-operativeurl <- "http://www.ebi.ac.uk/ols4/api/ontologies/cvdo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_3627/descendants"
aortic_aneurysm_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 6
[1] "\n Some example terms"
[1] "ruptured thoracoabdominal aortic aneurysm"
[2] "ruptured abdominal aortic aneurysm"
[3] "ruptured thoracic aortic aneurysm"
[4] "abdominal aortic aneurysm"
[5] "ruptured aortic aneurysm" gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(aortic_aneurysm_terms, collapse = "(?=,|$)|\\b"),
"aortic aneurysm"
)
)
gwas_study_info |>
filter(grepl("aortic aneurysm", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: thoracic aortic aneurysm, abdominal aortic aneurysm, brain aneurysm
2: abdominal aortic aneurysm
3: thoracic aortic aneurysm
4: aortic aneurysm
5: marfan syndrome, thoracic aortic aneurysm
l2_all_disease_terms
<char>
1: aortic aneurysm, brain aneurysm
2: aortic aneurysm
3: aortic aneurysm
4: aortic aneurysm
5: aortic aneurysm, marfan syndromegwas_study_info |>
filter(grepl("lower extremity peripheral arterial disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsgwas_study_info |>
filter(grepl("endocarditis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: staphylococcus aureus infection, bacterial endocarditis
2: endocarditis
l2_all_disease_terms
<char>
1: endocarditis, staphylococcus aureus infection
2: endocarditisother_cardiovascular_terms <- c("tachycardia",
"other cardiac arrhythmias",
"heart block",
"atrioventricular canal defect",
"abnormality of the cardiovascular system",
"abnormal cardiac septum morphology",
"congenital anomaly of cardiovascular system",
"carotid artery disease",
"abnormal cardiovascular system physiology",
"abnormal cardiovascular system morphology",
"pericarditis",
"congenital anomaly of the great arteries",
"coronary artery calcification",
"arterial embolism",
"arterial thrombosis"
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(other_cardiovascular_terms, collapse = "(?=,|$)|\\b"),
"other cardiovascular and circulatory diseases"
)
)
gwas_study_info |>
filter(grepl("other cardiovascular and circulatory diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: type 2 diabetes mellitus, coronary artery calcification
2: cardiac arrhythmia
3: coronary artery calcification
4: hiv-1 infection, carotid artery disease
5: sudden cardiac arrest
6: ventricular fibrillation
l2_all_disease_terms
<char>
1: other cardiovascular and circulatory diseases, type 2 diabetes mellitus
2: other cardiovascular and circulatory diseases
3: other cardiovascular and circulatory diseases
4: other cardiovascular and circulatory diseases, hiv infection
5: other cardiovascular and circulatory diseases
6: other cardiovascular and circulatory diseasesgwas_study_info |>
filter(grepl("chronic obstructive pulmonary disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: chronic obstructive pulmonary disease
2: chronic obstructive pulmonary disease, chronic bronchitis
3: digestive system carcinoma, chronic obstructive pulmonary disease
4: cancer, chronic obstructive pulmonary disease
5: lung carcinoma, chronic obstructive pulmonary disease
6: asthma, chronic obstructive pulmonary disease
l2_all_disease_terms
<char>
1: chronic obstructive pulmonary disease
2: chronic bronchitis, chronic obstructive pulmonary disease
3: chronic obstructive pulmonary disease, other malignant neoplasms
4: other malignant neoplasms, chronic obstructive pulmonary disease
5: chronic obstructive pulmonary disease, tracheal bronchus and lung cancer
6: asthma, chronic obstructive pulmonary diseasegwas_study_info |>
filter(grepl("pneumoconiosis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: pneumoconiosis pneumoconiosisgwas_study_info |>
filter(grepl("asthma", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: asthma
2: asthma, allergic disease
3: childhood onset asthma
4: childhood onset asthma, respiratory symptom change measurement
5: age of onset of asthma
6: aspirin-induced asthma
l2_all_disease_terms
<char>
1: asthma
2: allergic disease, asthma
3: asthma
4: asthma, respiratory symptom
5: asthma
6: asthmainterstitial_lung_disease_terms <- c("pulmonary sarcoidosis",
"interstitial lung disease"
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(interstitial_lung_disease_terms,
collapse = "(?=,|$)|\\b"),
"interstitial lung disease and pulmonary sarcoidosis"
)
)
gwas_study_info |>
filter(grepl("interstitial lung disease and pulmonary sarcoidosis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: rheumatoid arthritis, interstitial lung disease
2: interstitial lung disease
3: systemic scleroderma, interstitial lung disease
l2_all_disease_terms
<char>
1: interstitial lung disease and pulmonary sarcoidosis, rheumatoid arthritis
2: interstitial lung disease and pulmonary sarcoidosis
3: interstitial lung disease and pulmonary sarcoidosis, systemic sclerodermagwas_study_info |>
filter(grepl("other chronic respiratory diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsurl <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F328383001/descendants"
chronic_liver_disease_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 114
[1] "\n Some example terms"
[1] "hepatic ascites co-occurrent with chronic active hepatitis due to toxic liver disease"
[2] "cirrhosis of liver co-occurrent and due to primary sclerosing cholangitis (disorder)"
[3] "chronic hepatitis c co-occurrent with human immunodeficiency virus infection"
[4] "primary biliary cirrhosis co-occurrent with systemic scleroderma (disorder)"
[5] "pulmonary fibrosis, hepatic hyperplasia, bone marrow hypoplasia syndrome" chronic_liver_disease_terms <- c("primary biliary cirrhosis",
"alcoholic liver cirrhosis",
"chronic hepatitis B virus infection",
"acute-on-chronic liver failure",
chronic_liver_disease_terms)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(chronic_liver_disease_terms, collapse = "(?=,|$)|\\b"),
"cirrhosis and other chronic liver diseases"
)
)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "liver disease",
"cirrhosis and other chronic liver diseases"
)
)
gwas_study_info |>
filter(grepl("cirrhosis and other chronic liver diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: alcoholic liver cirrhosis, alcoholic pancreatitis, alcohol dependence
2: alcoholic liver cirrhosis, alcoholic pancreatitis
3: primary biliary cirrhosis
4: alagille syndrome, liver disease
5: alcoholic hepatitis
6: inflammatory bowel disease, liver disease
l2_all_disease_terms
<char>
1: alcohol-related disorders, alcoholic cirrhosis and other chronic liver diseases, pancreatitis
2: alcoholic cirrhosis and other chronic liver diseases, pancreatitis
3: cirrhosis and other chronic cirrhosis and other chronic liver diseasess
4: alagille syndrome, cirrhosis and other chronic liver diseases
5: alcoholic cirrhosis and other chronic liver diseases
6: inflammatory bowel disease, cirrhosis and other chronic liver diseasesupper_dig_terms <- c("peptic ulcer diseases",
"duodenitis",
"gastritis",
"gastroesophageal reflux disease")
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(upper_dig_terms, collapse = "(?=,|$)|\\b"),
"upper digestive system diseases"
)
)
gwas_study_info |>
filter(grepl("upper digestive system diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: gastroesophageal reflux disease
2: esophageal adenocarcinoma, gastroesophageal reflux disease
3: barretts esophagus, gastroesophageal reflux disease
4: gastritis
5: atrophic gastritis
6: gastroesophageal reflux disease, major depressive disorder
l2_all_disease_terms
<char>
1: upper digestive system diseases
2: esophageal cancer, upper digestive system diseases
3: barretts esophagus, upper digestive system diseases
4: upper digestive system diseases
5: atrophic upper digestive system diseases
6: upper digestive system diseases, major depressive disordergwas_study_info |>
filter(grepl("appendicitis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: appendicitis appendicitisgwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "\\bparalytic ileus\\b|\\bintestinal obstruction\\b",
"paralytic ileus and intestinal obstruction"
)
)
gwas_study_info |>
filter(grepl("paralytic ileus and intestinal obstruction", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: cystic fibrosis associated meconium ileus
2: intestinal obstruction
3: paralytic ileus
4: intestinal impaction
5: cystic fibrosis, cystic fibrosis associated meconium ileus
6: ileus
l2_all_disease_terms
<char>
1: paralytic ileus and intestinal obstruction
2: paralytic ileus and intestinal obstruction
3: paralytic ileus and intestinal obstruction
4: paralytic ileus and intestinal obstruction
5: cystic fibrosis, paralytic ileus and intestinal obstruction
6: paralytic ileus and intestinal obstructionhernia_terms <- c("inguinal hernia",
"femoral hernia",
"abdominal hernia",
"hernia of the abdominal wall")
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(hernia_terms, collapse = "(?=,|$)|\\b"),
"inguinal femoral and abdominal hernia"
)
)
gwas_study_info |>
filter(grepl("inguinal femoral and abdominal hernia", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: inguinal hernia inguinal femoral and abdominal hernia
2: hernia of the abdominal wall inguinal femoral and abdominal hernia
3: femoral hernia inguinal femoral and abdominal hernia
4: umbilical hernia inguinal femoral and abdominal hernia
5: ventral hernia inguinal femoral and abdominal hernia
6: incisional hernia inguinal femoral and abdominal herniaibd_terms <- c("crohns disease",
"ulcerative colitis",
"inflammatory bowel disease")
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(ibd_terms, collapse = "(?=,|$)|\\b"),
"inflammatory bowel disease"
)
)gwas_study_info |>
filter(grepl("vascular intestinal disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsgal_bile_terms = c("gallbladder disease",
"bile duct disorder",
"biliary tract disease")
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(gal_bile_terms, collapse = "(?=,|$)|\\b"),
"gallbladder and biliary diseases"
)
)
gwas_study_info |>
filter(grepl("gallbladder and biliary diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: bile duct disorder
2: gallbladder disease
3: biliary tract disease
4: non-neoplastic bile duct disorder
5: biliary tract disease, pancreas disease, liver disease
l2_all_disease_terms
<char>
1: gallbladder and biliary diseases
2: gallbladder and biliary diseases
3: gallbladder and biliary diseases
4: non-neoplastic gallbladder and biliary diseases
5: gallbladder and biliary diseases, cirrhosis and other chronic liver diseases, pancreas diseasegwas_study_info |>
filter(grepl("pancreatitis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: alcoholic liver cirrhosis, alcoholic pancreatitis, alcohol dependence
2: alcoholic liver cirrhosis, alcoholic pancreatitis
3: inflammatory bowel disease, pancreatitis
4: acute lymphoblastic leukemia, asparaginase-induced acute pancreatitis
5: autoimmune pancreatitis type 1, salivary gland lesion, lachrymal gland lesion
6: alcoholic pancreatitis
l2_all_disease_terms
<char>
1: alcohol-related disorders, alcoholic cirrhosis and other chronic liver diseases, pancreatitis
2: alcoholic cirrhosis and other chronic liver diseases, pancreatitis
3: inflammatory bowel disease, pancreatitis
4: leukemia, pancreatitis
5: lachrymal gland lesion, pancreatitis, salivary gland lesion
6: pancreatitisgwas_study_info |>
filter(grepl("other digestive diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsdementia <- c("alzheimers disease biomarker measurement",
"alzheimers disease neuropathologic change",
"aids dementia",
"dementia",
"frontotemporal dementia",
"lewy body dementia",
"vascular dementia",
"alzheimers disease"
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(dementia, collapse = "(?=,|$)|\\b"),
"alzheimer's disease and other dementias"
)
)
gwas_study_info |>
filter(grepl("alzheimer's disease and other dementias", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: alzheimer disease
2: age of onset of alzheimer disease
3: hypertension, alzheimer disease
4: family history of alzheimers disease
5: alzheimer disease, family history of alzheimers disease
6: lewy body dementia
l2_all_disease_terms
<char>
1: alzheimer's disease and other dementias
2: alzheimer's disease and other dementias
3: alzheimer's disease and other dementias, hypertension
4: alzheimer's disease and other dementias
5: alzheimer's disease and other dementias
6: alzheimer's disease and other dementiasgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "parkinsons disease",
"parkinson's disease"
)
)
gwas_study_info |>
filter(grepl("parkinson's disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: parkinson disease
2: age of onset of parkinson disease
3: frontotemporal dementia, parkinson disease
4: lewy body attribute, parkinson disease
5: schizophrenia, parkinson disease
6: dementia, parkinson disease, disease progression measurement
l2_all_disease_terms
<char>
1: parkinson's disease
2: parkinson's disease
3: alzheimer's disease and other dementias, parkinson's disease
4: alzheimer's disease and other dementias, parkinson's disease
5: parkinson's disease, schizophrenia
6: alzheimer's disease and other dementias, parkinson's diseasegwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "idiopathic generalized epilepsy",
"idiopathic epilepsy"
)
)
gwas_study_info |>
filter(grepl("idiopathic epilepsy", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: childhood absence epilepsy idiopathic epilepsy
2: juvenile absence epilepsy idiopathic epilepsy
3: juvenile myoclonic epilepsy idiopathic epilepsygwas_study_info |>
filter(grepl("multiple sclerosis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: multiple sclerosis
2: type 2 diabetes mellitus, multiple sclerosis
3: multiple sclerosis, chronic lymphocytic leukemia
4: diffuse large b-cell lymphoma, multiple sclerosis
5: follicular lymphoma, multiple sclerosis
6: marginal zone b-cell lymphoma, multiple sclerosis
l2_all_disease_terms
<char>
1: multiple sclerosis
2: multiple sclerosis, type 2 diabetes mellitus
3: leukemia, multiple sclerosis
4: multiple sclerosis, non-hodgkin lymphoma
5: multiple sclerosis, non-hodgkin lymphoma
6: multiple sclerosis, non-hodgkin lymphomagwas_study_info |>
filter(grepl("motor neuron disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: motor neuron disease motor neuron diseasegwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "\\bheadache disorder\\b|cluster headache\\b|migraine\\b",
"headache disorders"
)
)
gwas_study_info |>
filter(grepl("headache disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: migraine disorder, coronary artery disease
2: migraine without aura
3: migraine disorder
4: migraine with aura
5: cluster headache
6: bipolar disorder, migraine disorder
l2_all_disease_terms
<char>
1: ischemic heart disease, headache disorders
2: headache disorders
3: headache disorders
4: headache disorders
5: headache disorders
6: bipolar disorder, headache disordersgwas_study_info |>
filter(grepl("other neurological disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsgwas_study_info |>
filter(grepl("schizophrenia", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: schizophrenia
2: major depressive disorder, schizophrenia, bipolar disorder
3: schizophrenia, bipolar disorder
4: schizophrenia, major depressive disorder
5: schizophrenia, type 2 diabetes mellitus
6: treatment refractory schizophrenia, drug-induced agranulocytosis
l2_all_disease_terms
<char>
1: schizophrenia
2: bipolar disorder, major depressive disorder, schizophrenia
3: bipolar disorder, schizophrenia
4: major depressive disorder, schizophrenia
5: schizophrenia, type 2 diabetes mellitus
6: drug-induced agranulocytosis, schizophreniagwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "depressive symptom measurement|major depressive disorder",
"depressive disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "depressive disorder",
"depressive disorders"
)
)
gwas_study_info |>
filter(grepl("depressive disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: major depressive disorder
2: major depressive disorder, schizophrenia, bipolar disorder
3: major depressive disorder, bipolar disorder
4: bipolar disorder, major depressive disorder
5: schizophrenia, major depressive disorder
6: depressive symptom measurement, major depressive disorder
l2_all_disease_terms
<char>
1: depressive disorderss
2: bipolar disorder, depressive disorderss, schizophrenia
3: bipolar disorder, depressive disorderss
4: bipolar disorder, depressive disorderss
5: depressive disorderss, schizophrenia
6: depressive symptom, depressive disorderssurl <- "http://www.ebi.ac.uk/ols4/api/ontologies/mesh/terms/http%253A%252F%252Fid.nlm.nih.gov%252Fmesh%252FD001008/descendants"
anxiety_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 15
[1] "\n Some example terms"
[1] "obsessive-compulsive disorder" "generalized anxiety disorder"
[3] "neurocirculatory asthenia" "excoriation disorder"
[5] "anxiety, separation" anxiety_terms <- c(anxiety_terms, "obsessive-compulsive symptom measurement")
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(anxiety_terms, collapse = "(?=,|$)|\\b"),
"anxiety disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anxiety disorder|anxiety measurement",
"anxiety disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anxiety",
"anxiety disorders"
)
)
gwas_study_info |>
filter(grepl("anxiety disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: generalized anxiety disorder
2: obsessive-compulsive disorder, attention deficit hyperactivity disorder
3: anxiety disorder measurement
4: obsessive-compulsive disorder
5: anxiety disorder
6: obsessive-compulsive symptom measurement
l2_all_disease_terms
<char>
1: anxiety disorders disorderss
2: adhd, anxiety disorders disorderss
3: anxiety disorders disorders
4: anxiety disorders disorderss
5: anxiety disorders disorders
6: anxiety disorders disorderssgwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "bulimia nervosa|anorexia nervosa|binge eating|eating disorder",
"eating disorders"
)
) |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anorexia",
"eating disorders"
)
)
gwas_study_info |>
filter(grepl("eating disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: bipolar disorder, binge eating eating disorders, bipolar disorder
2: binge eating, bipolar disorder eating disorders, bipolar disorder
3: anorexia nervosa eating disorders
4: eating disorder eating disorders
5: bulimia nervosa eating disorders
6: bipolar disorder, eating disorder bipolar disorder, eating disordersgwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = "autism",
"autism spectrum disorders"
)
)
gwas_study_info |>
filter(grepl("autism spectrum disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: autism spectrum disorder symptom
2: asperger syndrome
3: autism spectrum disorder, schizophrenia
4: autism spectrum disorder
5: obsessive-compulsive disorder, autism spectrum disorder
6: autism
l2_all_disease_terms
<char>
1: autism spectrum disorders
2: autism spectrum disorders
3: autism spectrum disorders, schizophrenia
4: autism spectrum disorders
5: autism spectrum disorders, anxiety disorders disorderss
6: autism spectrum disordersgwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "adhd",
"attention-deficit/hyperactivity disorder"
)
)
gwas_study_info |>
filter(grepl("attention-deficit/hyperactivity disorder", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: obsessive-compulsive disorder, attention deficit hyperactivity disorder
2: attention deficit hyperactivity disorder
3: attention deficit hyperactivity disorder, oppositional defiant disorder measurement
4: attention deficit hyperactivity disorder, conduct disorder
5: attention deficit hyperactivity disorder, bipolar disorder, autism spectrum disorder, schizophrenia, major depressive disorder
6: attention deficit hyperactivity disorder, bipolar disorder
l2_all_disease_terms
<char>
1: attention-deficit/hyperactivity disorder, anxiety disorders disorderss
2: attention-deficit/hyperactivity disorder
3: attention-deficit/hyperactivity disorder, oppositional defiant disorder
4: attention-deficit/hyperactivity disorder, conduct disorder
5: attention-deficit/hyperactivity disorder, autism spectrum disorders, bipolar disorder, depressive disorderss, schizophrenia
6: attention-deficit/hyperactivity disorder, bipolar disordergwas_study_info |>
filter(grepl("conduct disorder", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: conduct disorder
2: attention deficit hyperactivity disorder, conduct disorder
3: attention deficit hyperactivity disorder, conduct disorder, oppositional defiant disorder
l2_all_disease_terms
<char>
1: conduct disorder
2: attention-deficit/hyperactivity disorder, conduct disorder
3: attention-deficit/hyperactivity disorder, conduct disorder, oppositional defiant disordergwas_study_info |>
filter(grepl("idiopathic developmental intellectual disability", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsother_mental_disorders <- c("manic or hypomanic episode",
"mental or behavioural disorder",
"mental disorder"
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(other_mental_disorders, collapse = "(?=,|$)|\\b"),
"other mental disorders"
)
)
gwas_study_info |>
filter(grepl("other mental disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: bipolar disorder, manic or hypomanic episode
2: bipolar disorder, mental or behavioural disorder, major depressive disorder
3: mental or behavioural disorder
4: mental or behavioural disorder, autoimmune disease
5: brain injury, mental or behavioural disorder
6: bipolar i disorder, manic or hypomanic episode
l2_all_disease_terms
<char>
1: bipolar disorder, other mental disorders
2: bipolar disorder, depressive disorderss, other mental disorders
3: other mental disorders
4: autoimmune disease, other mental disorders
5: brain injury, other mental disorders
6: bipolar disorder, other mental disordersgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "alcohol-related disorders|alcohol and nicotine codependence",
"alcohol use disorders"
)
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "alcohol use disorder",
"alcohol use disorders"
)
)
gwas_study_info |>
filter(grepl("alcohol use disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: alcohol dependence
2: alcoholic liver cirrhosis, alcoholic pancreatitis, alcohol dependence
3: alcohol dependence measurement
4: alcohol and nicotine codependence
5: alcohol withdrawal
6: age of onset of alcohol dependence
l2_all_disease_terms
<char>
1: alcohol use disorderss
2: alcohol use disorderss, alcoholic cirrhosis and other chronic liver diseases, pancreatitis
3: alcohol use disorderss
4: alcohol use disorderss
5: alcohol use disorderss
6: alcohol use disorderssgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "opioid dependence|opioid use disorder",
"opioid use disorders"
)
)
gwas_study_info |>
filter(grepl("opioid use disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: opioid dependence opioid use disorders
2: opioid use disorder opioid use disorders
3: opioid use disorder, opioid use disordersgwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "cocaine-related disorders",
"cocaine use disorders"
)
)
gwas_study_info |>
filter(grepl("cocaine use disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: cocaine dependence cocaine use disorders
2: cocaine use disorder cocaine use disordersgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "methamphetamine",
"amphetamine"
)
)
gwas_study_info |>
filter(grepl("amphetamine", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: methamphetamine dependence
2: methamphetamine-induced psychosis
3: alcohol dependence, heroin dependence, methamphetamine dependence
l2_all_disease_terms
<char>
1: amphetamine use disorders
2: amphetamine use disorders
3: alcohol use disorderss, heroin dependence, amphetamine use disordersgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "cannabis dependence",
"cannabis use disorders"
)
)
gwas_study_info |>
filter(grepl("cannabis use disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: cannabis dependence
2: cannabis dependence measurement
3: cannabis dependence, schizophrenia, substance abuse
4: cannabis dependence, substance abuse
5: hiv infection, cannabis dependence measurement
l2_all_disease_terms
<char>
1: cannabis use disorders
2: cannabis use disorders
3: cannabis use disorders, schizophrenia, substance abuse
4: cannabis use disorders, substance abuse
5: cannabis use disorders, hiv infectiongwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "heroin dependence|drug dependence|nictone dependence|substance abuse|drug misuse|alcohol use disorders delirium",
"other drug use disorders"
)
)
gwas_study_info |>
filter(grepl("other drug use disorders", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: heroin dependence
2: drug dependence
3: substance abuse
4: cannabis dependence, schizophrenia, substance abuse
5: cannabis dependence, substance abuse
6: alcohol dependence, heroin dependence, methamphetamine dependence
l2_all_disease_terms
<char>
1: other drug use disorders
2: other drug use disorders
3: other drug use disorders
4: cannabis use disorders, schizophrenia, other drug use disorders
5: cannabis use disorders, other drug use disorders
6: alcohol use disorderss, other drug use disorders, amphetamine use disordersgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "type 1 diabetes mellitus",
"diabetes mellitus type 1"
)
)
gwas_study_info |>
filter(grepl("diabetes mellitus type 1", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: type 1 diabetes mellitus
2: autoimmune thyroid disease, systemic lupus erythematosus, type 1 diabetes mellitus, ankylosing spondylitis, psoriasis, common variable immunodeficiency, celiac disease, ulcerative colitis, crohns disease, autoimmune disease, juvenile idiopathic arthritis
3: rheumatoid arthritis, type 1 diabetes mellitus, psoriasis, celiac disease, ulcerative colitis, crohns disease, progressive supranuclear palsy
4: rheumatoid arthritis, amyotrophic lateral sclerosis, type 1 diabetes mellitus, psoriasis, celiac disease, ulcerative colitis, crohns disease
5: rheumatoid arthritis, type 1 diabetes mellitus, corticobasal degeneration disorder, psoriasis, celiac disease, ulcerative colitis, crohns disease
6: type 1 diabetes mellitus, type 2 diabetes mellitus, neuropathy, diabetic foot
l2_all_disease_terms
<char>
1: diabetes mellitus type 1
2: ankylosing spondylitis, autoimmune disease, autoimmune thyroid disease, celiac disease, common variable immunodeficiency, inflammatory bowel disease, juvenile idiopathic arthritis, psoriasis, systemic lupus erythematosus, diabetes mellitus type 1, inflammatory bowel disease
3: celiac disease, inflammatory bowel disease, progressive supranuclear palsy, psoriasis, rheumatoid arthritis, diabetes mellitus type 1, inflammatory bowel disease
4: amyotrophic lateral sclerosis, celiac disease, inflammatory bowel disease, psoriasis, rheumatoid arthritis, diabetes mellitus type 1, inflammatory bowel disease
5: celiac disease, corticobasal degeneration disorder, inflammatory bowel disease, psoriasis, rheumatoid arthritis, diabetes mellitus type 1, inflammatory bowel disease
6: diabetic foot, neuropathy, diabetes mellitus type 1, type 2 diabetes mellitusgwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "type 2 diabetes mellitus",
"diabetes mellitus type 2"
)
)
gwas_study_info |>
filter(grepl("diabetes mellitus type 2", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: type 2 diabetes mellitus
2: type 2 diabetes mellitus, multiple sclerosis
3: type 2 diabetes mellitus, diabetic maculopathy
4: type 2 diabetes mellitus, obesity, coronary artery disease
5: schizophrenia, type 2 diabetes mellitus
6: alzheimer disease, type 2 diabetes mellitus, coronary artery disease
l2_all_disease_terms
<char>
1: diabetes mellitus type 2
2: multiple sclerosis, diabetes mellitus type 2
3: diabetic eye disease, diabetes mellitus type 2
4: ischemic heart disease, obesity, diabetes mellitus type 2
5: schizophrenia, diabetes mellitus type 2
6: alzheimer's disease and other dementias, ischemic heart disease, diabetes mellitus type 2gwas_study_info |>
filter(grepl("chronic kidney disease", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsgwas_study_info |>
filter(grepl("acute glomerulonephritis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsgwas_study_info |>
filter(grepl("dermatitis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: pemphigus foliaceus dermatitis
2: pemphigus dermatitis
3: pemphigus vulgaris dermatitis
4: seborrheic dermatitis dermatitis
5: atopic eczema dermatitis
6: contact dermatitis due to nickel dermatitisgwas_study_info |>
filter(grepl("psoriasis", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: psoriasis
2: autoimmune thyroid disease, systemic lupus erythematosus, type 1 diabetes mellitus, ankylosing spondylitis, psoriasis, common variable immunodeficiency, celiac disease, ulcerative colitis, crohns disease, autoimmune disease, juvenile idiopathic arthritis
3: cutaneous psoriasis measurement, psoriasis
4: psoriasis vulgaris
5: psoriatic arthritis
6: cutaneous psoriasis measurement, psoriatic arthritis, psoriasis
l2_all_disease_terms
<char>
1: psoriasis
2: ankylosing spondylitis, autoimmune disease, autoimmune thyroid disease, celiac disease, common variable immunodeficiency, inflammatory bowel disease, juvenile idiopathic arthritis, psoriasis, systemic lupus erythematosus, diabetes mellitus type 1, inflammatory bowel disease
3: psoriasis
4: psoriasis
5: psoriasis
6: psoriasisgwas_study_info |>
filter(grepl("bacterial skin diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsgwas_study_info |>
filter(grepl("scabies", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsgwas_study_info |>
filter(grepl("fungal skin diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsgwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "acne",
"acne vulgaris"
)
)
gwas_study_info |>
filter(grepl("acne vulgaris", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: acne acne vulgarisgwas_study_info |>
filter(grepl("pruritus", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: non-alcoholic steatohepatitis, pruritus
2: pruritus
l2_all_disease_terms
<char>
1: non-alcoholic fatty cirrhosis and other chronic liver diseases, pruritus
2: pruritusgwas_study_info |>
filter(grepl("urticaria", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: urticaria, angioedema angioedema, urticaria
2: urticaria urticariagwas_study_info |>
filter(grepl("decubitus ulcer", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms l2_all_disease_terms
<char> <char>
1: decubitus ulcer decubitus ulcergwas_study_info |>
filter(grepl("other skin and subcutaneous diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsvision_loss_terms <- c("blindness",
"color vision disorder",
"vision disorder",
"myopia",
"refractive error",
"hyperopia",
"astigmatism",
"corneal astigmatism",
"presbyopia",
"anisometropia",
"esotropia",
"non-accomodative esotropia",
"accommodative esotropia")
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = paste0(vision_loss_terms, collapse = "(?=,|$)|\\b"),
"blindness and vision loss"
)
)
gwas_study_info |>
filter(grepl("blindness and vision loss", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head() all_disease_terms
<char>
1: refractive error
2: refractive error, age of onset of myopia
3: esotropia
4: accommodative esotropia
5: hyperopia
6: non-accomodative esotropia
l2_all_disease_terms
<char>
1: blindness and vision loss
2: abnormality of refraction, blindness and vision loss
3: blindness and vision loss
4: blindness and vision loss
5: blindness and vision loss
6: blindness and vision lossgwas_study_info |>
filter(grepl("other sense organ diseases", l2_all_disease_terms)) |>
select(all_disease_terms, l2_all_disease_terms) |>
distinct() |>
head()Empty data.table (0 rows and 2 cols): all_disease_terms,l2_all_disease_termsdiseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l2_all_disease_terms) |>
unlist() |>
stringr::str_trim()
pregnancy_terms <- grep("pregnancy", diseases, value = T)
gyno_terms <- c("endometriosis","placenta disease", pregnancy_terms)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(gyno_terms, collapse = "(?=,|$)|\\b"),
"gynecological diseases"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002028/descendants"
personality_disorders <- get_descendants(url)[1] "Number of terms collected:"
[1] 10
[1] "\n Some example terms"
[1] "obsessive-compulsive personality disorder"
[2] "narcissistic personality disorder"
[3] "schizotypal personality disorder"
[4] "histrionic personality disorder"
[5] "antisocial personality disorder" gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(personality_disorders, collapse = "(?=,|$)|\\b"),
"personality disorders"
)
)url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_535/descendants"
sleep_disorders <- get_descendants(url)[1] "Number of terms collected:"
[1] 16
[1] "\n Some example terms"
[1] "periodic limb movement disorder" "advanced sleep phase syndrome 3"
[3] "advanced sleep phase syndrome 2" "advanced sleep phase syndrome 1"
[5] "advanced sleep phase syndrome 4"url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0008568/descendants"
other_sleep_disorders <- get_descendants(url)[1] "Number of terms collected:"
[1] 26
[1] "\n Some example terms"
[1] "autosomal dominant cerebellar ataxia, deafness and narcolepsy"
[2] "hereditary sensory neuropathy-deafness-dementia syndrome"
[3] "rapid eye movement sleep disorder"
[4] "substance-induced sleep disorder"
[5] "drug induced central sleep apnea" sleep_disorders <- c(sleep_disorders,
other_sleep_disorders)
gwas_study_info = gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms,
pattern = paste0(sleep_disorders, collapse = "(?=,|$)|\\b"),
"sleep disorders"
)
)other_neuro <- c("mild neurocognitive disorder",
"hiv-associated neurocognitive disorder")gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "disorderss",
"disorders"
)
)
gwas_study_info =
gwas_study_info |>
mutate(l2_all_disease_terms =
stringr::str_replace_all(l2_all_disease_terms ,
pattern = "anxiety disorders disorderss",
"anxiety disorders"
)
)gbd_data <- data.table::fread(here::here("data/gbd/ihme_gbd_2019_global_disease_burden_rate_all_ages.csv"))
gbd_data$cause <- stringr::str_remove_all(gbd_data$cause, ",")
diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l2_all_disease_terms[gwas_study_info$l2_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
gbd_data$cause[!tolower(gbd_data$cause) %in% unique(diseases)] |> sort() |> unique() [1] "Acute glomerulonephritis"
[2] "Bacterial skin diseases"
[3] "Chronic kidney disease"
[4] "Congenital birth defects"
[5] "Drug use disorders"
[6] "Endocrine metabolic blood and immune disorders"
[7] "Fungal skin diseases"
[8] "Hemoglobinopathies and hemolytic anemias"
[9] "Idiopathic developmental intellectual disability"
[10] "Lower extremity peripheral arterial disease"
[11] "Oral disorders"
[12] "Other chronic respiratory diseases"
[13] "Other digestive diseases"
[14] "Other musculoskeletal disorders"
[15] "Other neurological disorders"
[16] "Other sense organ diseases"
[17] "Other skin and subcutaneous diseases"
[18] "Scabies"
[19] "Sudden infant death syndrome"
[20] "Total burden related to Non-alcoholic fatty liver disease (NAFLD)"
[21] "Urinary diseases and male infertility"
[22] "Vascular intestinal disorders"
[23] "Viral skin diseases" gbd_data =
gbd_data |>
mutate(cause = tolower(cause))
gwas_disease_traits = data.frame(cause = diseases)
# gwas_study_info |>
# filter(DISEASE_STUDY == T) |>
# select(all_disease_terms, l1_all_disease_terms, cause = l2_all_disease_terms) |>
# distinct()
left_join(gwas_disease_traits,
gbd_data) |>
head()Joining with `by = join_by(cause)`Warning in left_join(gwas_disease_traits, gbd_data): Detected an unexpected many-to-many relationship between `x` and `y`.
ℹ Row 1 of `x` matches multiple rows in `y`.
ℹ Row 19 of `y` matches multiple rows in `x`.
ℹ If a many-to-many relationship is expected, set `relationship =
"many-to-many"` to silence this warning. cause measure
1 cardiomyopathy and myocarditis DALYs (Disability-Adjusted Life Years)
2 cardiomyopathy and myocarditis Prevalence
3 cardiomyopathy and myocarditis Incidence
4 cleft lip <NA>
5 tracheal bronchus and lung cancer DALYs (Disability-Adjusted Life Years)
6 tracheal bronchus and lung cancer Prevalence
location sex age metric year val upper lower
1 Global Both All ages Rate 2019 150.76987 161.64731 141.45397
2 Global Both All ages Rate 2019 66.58115 76.02025 56.74068
3 Global Both All ages Rate 2019 16.48141 20.20195 13.42862
4 <NA> <NA> <NA> <NA> NA NA NA NA
5 Global Both All ages Rate 2019 580.36100 627.79984 532.74652
6 Global Both All ages Rate 2019 40.27440 43.51721 37.12978gwas_study_info |> select(cause = l2_all_disease_terms) |>
distinct() |>
left_join(gbd_data) |>
head()Joining with `by = join_by(cause)` cause measure
<char> <char>
1: <NA>
2: cardiomyopathy and myocarditis DALYs (Disability-Adjusted Life Years)
3: cardiomyopathy and myocarditis Prevalence
4: cardiomyopathy and myocarditis Incidence
5: cleft lip <NA>
6: tracheal bronchus and lung cancer DALYs (Disability-Adjusted Life Years)
location sex age metric year val upper lower
<char> <char> <char> <char> <int> <num> <num> <num>
1: <NA> <NA> <NA> <NA> NA NA NA NA
2: Global Both All ages Rate 2019 150.76987 161.64731 141.45397
3: Global Both All ages Rate 2019 66.58115 76.02025 56.74068
4: Global Both All ages Rate 2019 16.48141 20.20195 13.42862
5: <NA> <NA> <NA> <NA> NA NA NA NA
6: Global Both All ages Rate 2019 580.36100 627.79984 532.74652diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$l2_all_disease_terms[gwas_study_info$l2_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 1564# 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)
kidney disease hypertension
10915 7091
diabetes mellitus type 2 ischemic heart disease
922 570
other neoplasms depressive disorders
548 513
alzheimer's disease and other dementias breast cancer
509 379
schizophrenia asthma
368 348 gwas_study_info <- fwrite(gwas_study_info,
here::here("output/gwas_cat/gwas_study_info_trait_group_l2.csv"))
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] jsonlite_2.0.0 httr_1.4.7 stringr_1.5.1 ggplot2_3.5.2
[5] data.table_1.17.8 dplyr_1.1.4 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 compiler_4.3.1 renv_1.0.3 promises_1.3.3
[5] tidyselect_1.2.1 Rcpp_1.1.0 git2r_0.36.2 callr_3.7.6
[9] later_1.4.2 jquerylib_0.1.4 scales_1.4.0 yaml_2.3.10
[13] fastmap_1.2.0 here_1.0.1 R6_2.6.1 generics_0.1.4
[17] curl_6.4.0 knitr_1.50 tibble_3.3.0 rprojroot_2.1.0
[21] RColorBrewer_1.1-3 bslib_0.9.0 pillar_1.11.0 rlang_1.1.6
[25] cachem_1.1.0 stringi_1.8.7 httpuv_1.6.16 xfun_0.52
[29] getPass_0.2-4 fs_1.6.6 sass_0.4.10 cli_3.6.5
[33] withr_3.0.2 magrittr_2.0.3 ps_1.9.1 grid_4.3.1
[37] digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1 lifecycle_1.0.4
[41] vctrs_0.6.5 evaluate_1.0.4 glue_1.8.0 farver_2.1.2
[45] whisker_0.4.1 rmarkdown_2.29 tools_4.3.1 pkgconfig_2.0.3
[49] htmltools_0.5.8.1