Last updated: 2025-09-23
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | a78628a | IJbeasley | 2025-09-23 | More icd codes for infectious disease |
| html | bdcc9eb | IJbeasley | 2025-09-22 | Build site. |
| Rmd | f897b13 | IJbeasley | 2025-09-22 | More typo + structure fixing … |
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| html | a241ae1 | IJbeasley | 2025-09-22 | Build site. |
| Rmd | 62b9234 | IJbeasley | 2025-09-22 | Excluding infectious disease |
library(dplyr)
library(data.table)
library(stringr)source(here::here("code/get_term_descendants.R"))gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_disease_trait_simplified.csv"))diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms[gwas_study_info$collected_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 2187gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("hiv-1 infection"),
"hiv infection"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("hiv infection")
)
)gwas_study_info |>
filter(grepl("syphi", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("chlamydophila infectious disease")
)
)gwas_study_info |>
filter(grepl("gonorrhea", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("trichomoniasis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("herpes", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms) DISEASE/TRAIT
<char>
1: Shingles
2: Source of report of B02 (zoster [herpes zoster]) (UKB data field 130179)
3: ICD10 B02: Zoster [herpes zoster]
4: Herpes zoster (PheCode 53)
5: Herpes zoster with nervous system complications (PheCode 53.1)
6: Herpes simplex (PheCode 54)
7: Herpes zoster
8: Herpes simplex (PheCode 54)
9: Herpes zoster with nervous system complications (PheCode 53.1)
10: Herpes zoster with nervous system complications (PheCode 53.1)
11: Herpes zoster with nervous system complications (PheCode 53.1)
12: Herpes zoster (PheCode 53)
13: Herpes zoster (PheCode 53)
14: Herpes zoster (PheCode 53)
15: Herpes zoster (PheCode 53)
16: Herpes zoster with nervous system complications (PheCode 53.1)
17: Herpes simplex (PheCode 54)
18: Herpes simplex (PheCode 54)
19: Herpes simplex (PheCode 54)
20: Shingles
21: ICD10 B00: Herpesviral [herpes simplex] infections
22: ICD10 B02: Zoster [herpes zoster]
23: Response to tofacitinib treatment in rheumatoid arthritis (herpes zoster)(time to event)
24: Response to tofacitinib treatment in psoriasis (herpes zoster)(time to event)
25: Response to tofacitinib treatment in rheumatoid arthritis (herpes zoster)
26: Response to tofacitinib treatment in psoriasis (herpes zoster)
27: Response to tofacitinib treatment (herpes zoster)(time to event)
28: Response to tofacitinib treatment (herpes zoster)
29: ICD10 B00: Herpesviral [herpes simplex] infections (Gene-based burden)
30: ICD10 B02: Zoster [herpes zoster] (Gene-based burden)
31: Zoster infection
32: Herpes infection
33: Zoster infection
34: Herpes infection
DISEASE/TRAIT
collected_all_disease_terms
<char>
1: herpes zoster
2: herpes zoster
3: herpes zoster
4: herpes zoster
5: herpes zoster, nervous system disease, complication
6: herpes simplex infection
7: herpes zoster
8: herpes simplex infection
9: herpes zoster, nervous system disease, complication
10: herpes zoster, nervous system disease, complication
11: herpes zoster, nervous system disease, complication
12: herpes zoster
13: herpes zoster
14: herpes zoster
15: herpes zoster
16: herpes zoster, nervous system disease, complication
17: herpes simplex infection
18: herpes simplex infection
19: herpes simplex infection
20: herpes zoster
21: herpesviridae infectious disease
22: herpes zoster
23: rheumatoid arthritis, herpes zoster
24: psoriasis, herpes zoster
25: rheumatoid arthritis, herpes zoster
26: psoriasis, herpes zoster
27: psoriasis, rheumatoid arthritis, herpes zoster
28: psoriasis, rheumatoid arthritis, herpes zoster
29: herpesviridae infectious disease
30: herpes zoster
31: herpes zoster
32: herpes simplex infection
33: herpes zoster
34: herpes simplex infection
collected_all_disease_termsurl <- "http://www.ebi.ac.uk/ols4/api/ontologies/mesh/terms/http%253A%252F%252Fid.nlm.nih.gov%252Fmesh%252FD012749/descendants"
sti_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 36
[1] "\n Some example terms"
[1] "sexually transmitted diseases, bacterial"
[2] "aids arteritis, central nervous system"
[3] "hiv-associated lipodystrophy syndrome"
[4] "aids-related opportunistic infections"
[5] "sexually transmitted diseases, viral" for(term in sti_terms){
if(sum(grepl(term, gwas_study_info$collected_all_disease_terms)) > 0) {
print(paste0("Term removed:", term))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(term)
)
)
}
}[1] "Term removed:warts"tb_terms <- c("mycobacterium tuberculosis infection",
"pulmonary tuberculosis",
"extrapulmonary tuberculosis",
"meningeal tuberculosis")
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(tb_terms),
"tuberculosis"
))# acute lower respiratory infections
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F195742007/descendants"
# in the case of acute / chronic bronchitis, we will remove only acute
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("acute bronchitis", `DISEASE/TRAIT`, ignore.case = T) &
grepl(vec_to_grep_pattern("bronchitis"),
collected_all_disease_terms,
ignore.case = T,
perl = T),
stringr::str_remove_all(collected_all_disease_terms,
vec_to_grep_pattern("bronchitis")),
collected_all_disease_terms
))
# if bronchitis is specified as chronic in DISEASE/TRAIT, replace bronchitis with chronic bronchitis
# in to collected_all_disease_terms
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("chronic bronchitis", `DISEASE/TRAIT`, ignore.case = T) &
grepl(vec_to_grep_pattern("bronchitis"),
collected_all_disease_terms,
ignore.case = T,
perl = T),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("bronchitis"),
"chronic bronchitis"),
collected_all_disease_terms
))
# similar, for bronchiolitis, remove if acute
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("acute bronchiolitis", `DISEASE/TRAIT`, ignore.case = T) &
grepl(vec_to_grep_pattern("bronchiolitis"),
collected_all_disease_terms,
ignore.case = T,
perl = T),
stringr::str_remove_all(collected_all_disease_terms,
vec_to_grep_pattern("bronchiolitis")),
collected_all_disease_terms
))
lri_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 35
[1] "\n Some example terms"
[1] "chronic obstructive pulmonary disease with acute lower respiratory infection"
[2] "acute lower respiratory infection caused by respiratory syncytial virus"
[3] "acute infective exacerbation of chronic obstructive pulmonary disease"
[4] "inflammation of bronchiole caused by human metapneumovirus"
[5] "acute bronchiolitis caused by respiratory syncytial virus" lri_terms <- c("acute bronchitis",
"respiratory syncytial virus infection",
lri_terms
)
for(term in lri_terms){
if(sum(grepl(term, gwas_study_info$collected_all_disease_terms)) > 0) {
print(paste0("Term removed:", term))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(term)
)
)
}
}[1] "Term removed:acute bronchitis"
[1] "Term removed:respiratory syncytial virus infection"# remove larygitis, if acute
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("acute laryngitis", `DISEASE/TRAIT`, ignore.case = T) &
grepl(vec_to_grep_pattern("laryngitis"),
collected_all_disease_terms,
ignore.case = T,
perl = T),
stringr::str_remove_all(collected_all_disease_terms,
vec_to_grep_pattern("laryngitis")),
collected_all_disease_terms
))
# if laryngitis is specified as chronic in DISEASE/TRAIT, replace laryngitis with chronic laryngitis
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("chronic laryngitis", `DISEASE/TRAIT`, ignore.case = T) &
grepl(vec_to_grep_pattern("laryngitis"),
collected_all_disease_terms,
ignore.case = T,
perl = T),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("laryngitis"),
"chronic laryngitis"),
collected_all_disease_terms
))
# for tonsillitis, remove if acute
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("acute tonsillitis|ICD10 J03", `DISEASE/TRAIT`, ignore.case = T) &
grepl(vec_to_grep_pattern("tonsillitis"),
collected_all_disease_terms,
ignore.case = T,
perl = T),
stringr::str_remove_all(collected_all_disease_terms,
vec_to_grep_pattern("tonsillitis")),
collected_all_disease_terms
))
# for tonsillitis, if chronic in DISEASE/TRAIT, replace tonsillitis with chronic tonsillitis
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("chronic tonsillitis", `DISEASE/TRAIT`, ignore.case = T) &
grepl(vec_to_grep_pattern("tonsillitis"),
collected_all_disease_terms,
ignore.case = T,
perl = T),
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("tonsillitis"),
"chronic tonsillitis"),
collected_all_disease_terms
))
# acute upper respiratory infections
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/snomed/terms/http%253A%252F%252Fsnomed.info%252Fid%252F54398005/descendants"
uri_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 30
[1] "\n Some example terms"
[1] "acute upper respiratory infection caused by respiratory syncytial virus"
[2] "acute infective pharyngitis caused by streptococcus (disorder)"
[3] "acute nasopharyngitis caused by respiratory syncytial virus"
[4] "acute laryngitis caused by haemophilus influenzae"
[5] "fusobacterial necrotizing tonsillitis (disorder)" uri_terms <- c("strep throat",
"streptococcal pharyngitis",
"acute pharyngitis",
"pharyngitis",
"acute tonsillitis",
uri_terms
)
for(term in uri_terms){
if(sum(grepl(term, gwas_study_info$collected_all_disease_terms)) > 0) {
print(paste0("Term removed:", term))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(term)
)
)
}
}[1] "Term removed:strep throat"
[1] "Term removed:streptococcal pharyngitis"
[1] "Term removed:acute pharyngitis"
[1] "Term removed:pharyngitis"
[1] "Term removed:acute tonsillitis"url <- "http://www.ebi.ac.uk/ols4/api/ontologies/doid/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FDOID_10754/descendants"
otitis_media_terms <- get_descendants(url)[1] "Number of terms collected:"
[1] 20
[1] "\n Some example terms"
[1] "chronic tubotympanic suppurative otitis media"
[2] "acute allergic sanguinous otitis media"
[3] "acute allergic mucoid otitis media"
[4] "acute allergic serous otitis media"
[5] "middle ear cholesterol granuloma" gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(otitis_media_terms),
"otitis media"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("otitis media")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("covid-19")
)
)gwas_study_info = gwas_study_info |>
mutate(l1_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("influenza a \\(h1n1\\)"),
"influenza"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("influenza")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("astroviridae infectious disease, infantile diarrhea")
)
)
# if diarrhea is caused by IBS, add ibs to collected_all_disease_terms
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("IBS", `DISEASE/TRAIT`, ignore.case = T) &
grepl("diarrhea", collected_all_disease_terms, ignore.case = T),
paste0(collected_all_disease_terms, ", irritable bowel syndrome"),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("typhoid fever")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("non-typhoidal salmonella bacteremia")
)
)# remove bacterial and viral gastroenteritis
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("gastroenteritis", collected_all_disease_terms, ignore.case = T) &
grepl("bacterial gastroenteritis|viral gastroenteritis",
collected_all_disease_terms,
ignore.case = T),
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("gastroenteritis")
),
collected_all_disease_terms
)
)# remove viral and bacterial enteritis
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("enteritis", collected_all_disease_terms, ignore.case = T) &
grepl("bacterial enteritis|viral enteritis",
collected_all_disease_terms,
ignore.case = T),
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("enteritis")
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("intestinal infectious disease")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern(
c("plasmodium falciparum malaria",
"plasmodium vivax malaria"
)),
"malaria"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("malaria")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("chagas disease")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("visceral leishmaniasis")
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("cutaneous leishmaniasis")
)
)gwas_study_info |>
filter(grepl("trypanosomiasis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("schistosomiasis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("cysticercosis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("echinococcosis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("filariasis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("onchocerciasis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("trachoma", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("dengue hemorrhagic fever"),
"dengue"
))
gwas_study_info |>
filter(grepl("dengue", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms) DISEASE/TRAIT collected_all_disease_terms
<char> <char>
1: Dengue shock syndrome denguegwas_study_info |>
filter(grepl("yellow fever", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("rabies", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_terms# ascariasis
gwas_study_info |>
filter(grepl("ascariasis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_terms# trichuriasis
gwas_study_info |>
filter(grepl("trichuriasis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_terms# hookworm
gwas_study_info |>
filter(grepl("hookworm", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("trema", collected_all_disease_terms, ignore.case = T)
) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("leprosy", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms) |>
distinct() DISEASE/TRAIT collected_all_disease_terms
<char> <char>
1: Leprosy leprosy
2: Crohn's disease or Leprosy leprosy, crohns disease
3: Crohn's disease or Leprosy (opposite effect) leprosy, crohns diseasegwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("leprosy")
)
)gwas_study_info |>
filter(grepl("ebola", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("zika", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms) DISEASE/TRAIT collected_all_disease_terms
<char> <char>
1: Congenital Zika syndrome zika virus congenital syndromegwas_study_info |>
filter(grepl("worm", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsmeningitis_terms <- c(
"meningococcal infection",
"infectious meningitis",
"bacterial meningitis",
"viral meningitis",
"pneumococcal meningitis",
"meningitis"
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(meningitis_terms)
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("viral encephalitis")
)
)
# ? also remove if DISEASE/TRAIT == Encephalitis (PheCode 323)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(`DISEASE/TRAIT` == "Encephalitis (PheCode 323)",
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("encephalitis")
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("diphtheria")
)
)gwas_study_info |>
filter(grepl("pertussis", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms)Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info |>
filter(grepl("tetanus", collected_all_disease_terms, ignore.case = T)) |>
select(`DISEASE/TRAIT`, collected_all_disease_terms) Empty data.table (0 rows and 2 cols): DISEASE/TRAIT,collected_all_disease_termsgwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("measles")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("chickenpox")
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(`DISEASE/TRAIT` == "Herpes zoster (PheCode 53)" |
`DISEASE/TRAIT` == "Herpes zoster" |
`DISEASE/TRAIT` == "Zoster infection" |
grepl("ICD10 B02: Zoster \\[herpes zoster\\]", `DISEASE/TRAIT`),
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("herpes zoster")
),
collected_all_disease_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("complication, herpes zoster, nervous system disease"),
"herpes zoster, nervous system disease"
)
)# if acute hepatitis in DISEASE/TRAIT remove from collected_all_disease_terms
gwas_study_info |>
filter(grepl("acute hepat",
`DISEASE/TRAIT`,
ignore.case = T)) |>
pull(`DISEASE/TRAIT`) |>
unique()[1] "Acute hepatitis A infection"gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(`DISEASE/TRAIT` == "Acute hepatitis A infection",
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("hepatitis a infection")
),
collected_all_disease_terms
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("bacterial pneumonia")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("infectious mononucleosis")
)
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("epstein-barr virus infection")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("protozoa infectious disease")
)
)gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("herpes simplex", `DISEASE/TRAIT`, ignore.case = T) &
grepl("herpesviridae infectious disease", collected_all_disease_terms, ignore.case = T),
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("herpesviridae infectious disease"),
"herpes simplex infection"),
collected_all_disease_terms
)
)
# cold sores
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("cold sores"),
"herpes simplex infection"
)
)
gwas_study_info |>
filter(grepl("herpes", collected_all_disease_terms, ignore.case = T)) |>
pull(`DISEASE/TRAIT`) |>
unique() [1] "Cold sores"
[2] "Shingles"
[3] "Source of report of B02 (zoster [herpes zoster]) (UKB data field 130179)"
[4] "Herpes zoster with nervous system complications (PheCode 53.1)"
[5] "Herpes simplex (PheCode 54)"
[6] "ICD10 B00: Herpesviral [herpes simplex] infections"
[7] "Response to tofacitinib treatment in rheumatoid arthritis (herpes zoster)(time to event)"
[8] "Response to tofacitinib treatment in psoriasis (herpes zoster)(time to event)"
[9] "Response to tofacitinib treatment in rheumatoid arthritis (herpes zoster)"
[10] "Response to tofacitinib treatment in psoriasis (herpes zoster)"
[11] "Response to tofacitinib treatment (herpes zoster)(time to event)"
[12] "Response to tofacitinib treatment (herpes zoster)"
[13] "ICD10 B00: Herpesviral [herpes simplex] infections (Gene-based burden)"
[14] "Herpes infection" gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("mumps")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("parasitic infection")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("helicobacter pylori infectious disease")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("common cold")
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("tropical spastic paraparesis")
)
)# parasitic infectiongwas_study_info =
gwas_study_info |>
rowwise() |>
mutate(collected_all_disease_terms = paste0(sort(unique(unlist(strsplit(collected_all_disease_terms, ", ")))),
collapse = ", ")
) |>
ungroup()gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms = stringr::str_remove_all(collected_all_disease_terms, "^,|,$")
) |>
mutate(collected_all_disease_terms = stringr::str_trim(collected_all_disease_terms)
) n_studies_trait = gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(collected_all_disease_terms, PUBMED_ID) |>
dplyr::distinct() |>
dplyr::group_by(collected_all_disease_terms) |>
dplyr::summarise(n_studies = dplyr::n()) |>
dplyr::arrange(desc(n_studies))
head(n_studies_trait)# A tibble: 6 × 2
collected_all_disease_terms n_studies
<chr> <int>
1 "type 2 diabetes mellitus" 146
2 "" 120
3 "alzheimers disease" 116
4 "breast cancer" 113
5 "asthma" 111
6 "major depressive disorder" 109dim(n_studies_trait)[1] 2940 2diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms[gwas_study_info$collected_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 2127fwrite(gwas_study_info,
here::here("output/gwas_cat/gwas_study_info_disease_trait_filtered.csv"))
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] jsonlite_2.0.0 httr_1.4.7 stringr_1.5.1 data.table_1.17.8
[5] dplyr_1.1.4 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] compiler_4.3.1 renv_1.0.3 promises_1.3.3 tidyselect_1.2.1
[5] Rcpp_1.1.0 git2r_0.36.2 callr_3.7.6 later_1.4.2
[9] jquerylib_0.1.4 yaml_2.3.10 fastmap_1.2.0 here_1.0.1
[13] R6_2.6.1 generics_0.1.4 curl_6.4.0 knitr_1.50
[17] tibble_3.3.0 rprojroot_2.1.0 bslib_0.9.0 pillar_1.11.0
[21] rlang_1.1.6 utf8_1.2.6 cachem_1.1.0 stringi_1.8.7
[25] httpuv_1.6.16 xfun_0.52 getPass_0.2-4 fs_1.6.6
[29] sass_0.4.10 cli_3.6.5 withr_3.0.2 magrittr_2.0.3
[33] ps_1.9.1 digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1
[37] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.4 glue_1.8.0
[41] whisker_0.4.1 rmarkdown_2.29 tools_4.3.1 pkgconfig_2.0.3
[45] htmltools_0.5.8.1