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library(dplyr)
library(data.table)
library(stringr)source(here::here("code/get_term_descendants.R"))gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_disease_trait_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))gwas_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"
))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"
))# 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_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("bronchitis"),
"acute 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_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("bronchiolitis"),
"acute bronchiolitis"),
collected_all_disease_terms
))# 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_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("laryngitis"),
"acute laryngitis"),
collected_all_disease_terms
))
# if laryngitis is specified as acute in DISEASE/TRAIT, remove disease from collected_all_disease_terms
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("acute laryngitis", `DISEASE/TRAIT`, ignore.case = T) &
collected_all_disease_terms == "disease",
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("disease"),
"acute 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_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("tonsillitis"),
"acute tonsillitis"),
collected_all_disease_terms
))
# remove disease, if DISEASE/TRAIT contains acute tonsillitis
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("acute tonsillitis", `DISEASE/TRAIT`, ignore.case = T) &
collected_all_disease_terms == "disease",
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("disease"),
"acute 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
))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)
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"
))
# where collected_all_disease_terms==disease, and otitis media in DISEASE/TRAIT, remove disease
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(grepl("otitis media", `DISEASE/TRAIT`, ignore.case = T) &
collected_all_disease_terms == "disease",
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("disease"),
"otitis media"),
collected_all_disease_terms
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
vec_to_grep_pattern("influenza a \\(h1n1\\)"),
"influenza"
))# 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
)
)
# remove dysentery
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("dysentery")
)
)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_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern(c(
"visceral leishmaniasis",
"cutaneous leishmaniasis")
),
"leishmaniasis"
)
)gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
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)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
ifelse(`DISEASE/TRAIT` == "Acute hepatitis A infection",
stringr::str_replace_all(collected_all_disease_terms,
pattern = vec_to_grep_pattern("hepatitis a infection"),
"acute hepatitis a infection"
),
collected_all_disease_terms
)
)gwas_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, "^,|,$")
) |>
mutate(collected_all_disease_terms = stringr::str_trim(collected_all_disease_terms)
) n_studies_trait = gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(collected_all_disease_terms, PUBMED_ID) |>
dplyr::distinct() |>
dplyr::group_by(collected_all_disease_terms) |>
dplyr::summarise(n_studies = dplyr::n()) |>
dplyr::arrange(desc(n_studies))
head(n_studies_trait)
dim(n_studies_trait)diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms[gwas_study_info$collected_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))fwrite(gwas_study_info,
here::here("output/gwas_cat/gwas_study_info_disease_trait_filtered.csv"))
sessionInfo()