Last updated: 2025-08-25
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genomics_ancest_disease_dispar/
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knitr::opts_chunk$set(echo = TRUE,
message = FALSE,
warning = FALSE
)
library(data.table)
library(dplyr)
library(ggplot2)
library(stringr)library(httr)
library(jsonlite)url <-
"http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0700096/descendants"
mondo_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
mondo_descendants <- c(mondo_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(mondo_descendants)
mondo_descendants[1:5]
writeLines(mondo_descendants, here::here("output/trait_ontology/mondo_0700096_descendants.txt"))url <-
"http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000408/descendants"
efo_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
efo_descendants <- c(efo_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(efo_descendants)
efo_descendants[1:5]
writeLines(efo_descendants, here::here("output/trait_ontology/efo_0000408_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/ncit/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCIT_C2991/descendants"
ncit_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
ncit_descendants <- c(ncit_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(ncit_descendants)
ncit_descendants[1:5]
writeLines(ncit_descendants, here::here("output/trait_ontology/ncit_C2991_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/ordo/terms/http%253A%252F%252Fwww.orpha.net%252FORDO%252FOrphanet_557493/descendants"
orphanet_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
orphanet_descendants <- c(orphanet_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(orphanet_descendants)
orphanet_descendants[1:5]
writeLines(orphanet_descendants, here::here("output/trait_ontology/orphanet_557493_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_1110122/descendants"
path_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
path_descendants <- c(path_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(path_descendants)
path_descendants[1:5]
writeLines(path_descendants, here::here("output/trait_ontology/obi_1110122_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOGMS_0000063/descendants"
disease_course_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
disease_course_descendants <- c(disease_course_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(disease_course_descendants)
disease_course_descendants[1:5]
writeLines(disease_course_descendants, here::here("output/trait_ontology/ogms_0000063_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0000118/descendants"
hp_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
hp_descendants <- c(hp_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(hp_descendants)[1] 2625hp_descendants[1:5][1] "hypoxia"
[2] "necrosis"
[3] "Abnormality of limbs"
[4] "Abnormality of the musculoskeletal system"
[5] "Vocal cord dysfunction" writeLines(hp_descendants, here::here("output/trait_ontology/hp_0000118_descendants.txt"))# Define the API endpoint
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001444/descendants"
measurement_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
measurement_descendants <- c(measurement_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(measurement_descendants)
measurement_descendants[1:5]
writeLines(measurement_descendants, here::here("output/trait_ontology/efo_0001444_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0004574/descendants"
total_choles_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
total_choles_descendants <- c(total_choles_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
writeLines(total_choles_descendants, here::here("output/trait_ontology/efo_0004574_descendants.txt"))
length(total_choles_descendants)
total_choles_descendants[1:5]Includes:
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/go/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0050896/descendants"
go_response_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
go_response_descendants <- c(go_response_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(go_response_descendants)
go_response_descendants[1:5]
writeLines(go_response_descendants, here::here("output/trait_ontology/go_0050896_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0050896/descendants"
efo_response_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
efo_response_descendants <- c(efo_response_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(efo_response_descendants)
efo_response_descendants[1:5]
writeLines(efo_response_descendants, here::here("output/trait_ontology/efo_go_0050896_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000651/descendants"
phenotype_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
phenotype_descendants <- c(phenotype_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(phenotype_descendants)
phenotype_descendants[1:5]
writeLines(phenotype_descendants, here::here("output/trait_ontology/efo_0000651_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0004323/descendants"
mental_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
mental_descendants <- c(mental_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(mental_descendants)
mental_descendants[1:5]
mental_descendants = c("mental process",
"cognitive function measurement",
mental_descendants)
writeLines(mental_descendants, here::here("output/trait_ontology/efo_0004323_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0007610/descendants"
behavior_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
behavior_descendants <- c(behavior_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(behavior_descendants)
behavior_descendants[1:5]
behavior_descendants = c("behavior", behavior_descendants)
writeLines(behavior_descendants, here::here("output/trait_ontology/go_0007610_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000546/descendants"
injury_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
injury_descendants <- c(injury_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(injury_descendants)
injury_descendants[1:5]
injury_descendants = c("injury", injury_descendants)
writeLines(injury_descendants, here::here("output/trait_ontology/efo_0000546_descendants.txt"))enviro_factors <- c(
"income",
"socioeconomic status",
"encounter with health service related to socioeconomic and psychosocial circumstances" ,
"townsend deprivation index",
"household income",
"social deprivation",
"economic and social preference",
"social deprivation",
"physical activity",
"exercise",
"family relationship"
)gwas_study_info <- fread(here::here("output/gwas_study_info_cohort_corrected.csv"))all_gwas_terms = unique(gwas_study_info$MAPPED_TRAIT)
all_gwas_terms = stringr::str_trim(tolower(all_gwas_terms))efo_descendants <- readLines(here::here("output/trait_ontology/efo_0000408_descendants.txt"))
mondo_descendants <- readLines(here::here("output/trait_ontology/mondo_0700096_descendants.txt"))
ncit_descendants <- readLines(here::here("output/trait_ontology/ncit_C2991_descendants.txt"))
orphanet_descendants <- readLines(here::here("output/trait_ontology/orphanet_557493_descendants.txt"))
disease_terms = c(mondo_descendants,
efo_descendants,
ncit_descendants,
orphanet_descendants) |>
unique()
disease_terms = stringr::str_trim(tolower(disease_terms))
print("Number of terms related to disease or disorder")[1] "Number of terms related to disease or disorder"length(disease_terms)[1] 53251not_simple_disease_terms = all_gwas_terms[!all_gwas_terms %in% disease_terms]
# sometimes there's multiple terms - check if any disease term is in these gwas terms
multiple_terms = grep(",", not_simple_disease_terms, value = T)
mask <- Reduce(`|`, lapply(disease_terms, function(x) grepl(x, multiple_terms)))
additional_disease_gwas <- multiple_terms[mask]
disease_gwas = c(all_gwas_terms[all_gwas_terms %in% disease_terms],
additional_disease_gwas)
not_disease_terms = not_simple_disease_terms[!not_simple_disease_terms %in% additional_disease_gwas]
print("Number of GWAS traits under disease or disorder terms")[1] "Number of GWAS traits under disease or disorder terms"length(all_gwas_terms) - length(not_disease_terms)[1] 3377print("Percentage of GWAS traits under disease or disorder terms")[1] "Percentage of GWAS traits under disease or disorder terms"round(100 * (length(all_gwas_terms) - length(not_disease_terms)) / length(all_gwas_terms),
digits = 1)[1] 14.8print("Percentage of GWAS traits not under disease or disorder terms")[1] "Percentage of GWAS traits not under disease or disorder terms"round(100 * length(not_disease_terms) / length(all_gwas_terms),
digits = 1)[1] 85.2find_disease_terms = function(MAPPED_TRAIT) {
# find all disease terms that appear in the trait
split_mapped_traits <- stringr::str_split(MAPPED_TRAIT, ", ") |>
unlist()
mapped_disease_terms = disease_terms[disease_terms %in% split_mapped_traits]
mapped_disease_terms = unique(mapped_disease_terms)
return(paste0(mapped_disease_terms, collapse = ", ")) # combine multiple matches
}
gwas_study_info <-
gwas_study_info |>
dplyr::rowwise() |>
dplyr::mutate(
disease_terms =
ifelse(MAPPED_TRAIT %in% disease_gwas,
find_disease_terms(MAPPED_TRAIT),
NA)
)measurement <- readLines(here::here("output/trait_ontology/efo_0001444_descendants.txt"))
total_choles <- readLines(here::here("output/trait_ontology/efo_0004574_descendants.txt"))
measurement <- c(total_choles,
measurement)
measurement <- unique(measurement)
measurement = stringr::str_trim(tolower(measurement))# Find terms where all comma-split pieces are in measurement
measurement_gwas <- not_disease_terms[
sapply(strsplit(not_disease_terms, ", "), function(parts) {
parts <- trimws(parts) # remove extra spaces
all(parts %in% measurement)
})
]
additional_measurement <- not_disease_terms[not_disease_terms %in% measurement]
measurement_gwas = c(measurement_gwas, additional_measurement) |> unique()
print("Number of GWAS traits under measurement terms")[1] "Number of GWAS traits under measurement terms"length(measurement_gwas)[1] 18226print("Percentage of GWAS traits under measurement terms")[1] "Percentage of GWAS traits under measurement terms"round(100 * length(measurement_gwas) / length(all_gwas_terms),
digits = 1)[1] 79.7not_accounted_for = not_disease_terms[!not_disease_terms %in% measurement_gwas]
print("Percentage of GWAS traits not accounted for by disease, disorder or measurement terms")[1] "Percentage of GWAS traits not accounted for by disease, disorder or measurement terms"round(100 * length(not_accounted_for) / length(all_gwas_terms),
digits = 1)[1] 5.6print("Number of GWAS traits not accounted for by disease, disorder or measurement terms")[1] "Number of GWAS traits not accounted for by disease, disorder or measurement terms"length(not_accounted_for)[1] 1274go_response = readLines(here::here("output/trait_ontology/go_0050896_descendants.txt"))
efo_response <- readLines(here::here("output/trait_ontology/efo_go_0050896_descendants.txt"))
response <- c(go_response,
efo_response,
"response to stimulus")
response <- unique(response)
response = stringr::str_trim(tolower(response))response_gwas = not_accounted_for[not_accounted_for %in% response]
print("Percentage of GWAS traits under response terms")[1] "Percentage of GWAS traits under response terms"round(100 * length(response_gwas) / length(all_gwas_terms),
digits = 1)[1] 0.6not_accounted_for = not_accounted_for[!not_accounted_for %in% response_gwas]
print("Percentage of GWAS traits not accounted for by disease, measurement or response terms")[1] "Percentage of GWAS traits not accounted for by disease, measurement or response terms"round(100 * length(not_accounted_for) / length(all_gwas_terms),
digits = 1)[1] 5print("Number of GWAS traits not accounted for by disease, measurement or response terms")[1] "Number of GWAS traits not accounted for by disease, measurement or response terms"length(not_accounted_for)[1] 1141pheno_abnorm <- readLines(here::here("output/trait_ontology/hp_0000118_descendants.txt"))
pheno_abnorm = stringr::str_trim(tolower(pheno_abnorm))
pheno_abnorm_gwas = not_accounted_for[not_accounted_for %in% pheno_abnorm]
print("Percentage of GWAS traits under phenotype abnormality terms")[1] "Percentage of GWAS traits under phenotype abnormality terms"round(100 * length(pheno_abnorm_gwas) / length(all_gwas_terms),
digits = 1)[1] 1.5not_accounted_for = not_accounted_for[!not_accounted_for %in% pheno_abnorm_gwas]
print("Percentage of GWAS traits not accounted for so far")[1] "Percentage of GWAS traits not accounted for so far"round(100 * length(not_accounted_for) / length(all_gwas_terms),
digits = 1)[1] 3.5print("Number of GWAS traits not accounted for by so far")[1] "Number of GWAS traits not accounted for by so far"length(not_accounted_for)[1] 804mental <- readLines(here::here("output/trait_ontology/efo_0004323_descendants.txt"))
mental = stringr::str_trim(tolower(mental))
mental_gwas = not_accounted_for[not_accounted_for %in% mental]
print("Percentage of GWAS traits under mental process terms")[1] "Percentage of GWAS traits under mental process terms"round(100 * length(mental_gwas) / length(all_gwas_terms),
digits = 1)[1] 0.1not_accounted_for = not_accounted_for[!not_accounted_for %in% mental_gwas]
print("Percentage of GWAS traits not accounted for thus far")[1] "Percentage of GWAS traits not accounted for thus far"round(100 * length(not_accounted_for) / length(all_gwas_terms),
digits = 1)[1] 3.4print("Number of GWAS traits not accounted for thus far")[1] "Number of GWAS traits not accounted for thus far"length(not_accounted_for)[1] 786behavior <- readLines(here::here("output/trait_ontology/go_0007610_descendants.txt"))
behavior = stringr::str_trim(tolower(behavior))
behavior_gwas = not_accounted_for[not_accounted_for %in% behavior]
print("Percentage of GWAS traits under behavouir terms")[1] "Percentage of GWAS traits under behavouir terms"round(100 * length(behavior_gwas) / length(all_gwas_terms),
digits = 1)[1] 0.1not_accounted_for = not_accounted_for[!not_accounted_for %in% behavior_gwas]
print("Percentage of GWAS traits not accounted for so far")[1] "Percentage of GWAS traits not accounted for so far"round(100 * length(not_accounted_for) / length(all_gwas_terms),
digits = 1)[1] 3.3print("Number of GWAS traits not accounted for so far")[1] "Number of GWAS traits not accounted for so far"length(not_accounted_for)[1] 763injury <- readLines(here::here("output/trait_ontology/efo_0000546_descendants.txt"))
injury = stringr::str_trim(tolower(injury))
injury_gwas = not_accounted_for[not_accounted_for %in% injury]
print("Percentage of GWAS traits under injury terms")[1] "Percentage of GWAS traits under injury terms"round(100 * length(injury_gwas) / length(all_gwas_terms),
digits = 1)[1] 0.1not_accounted_for = not_accounted_for[!not_accounted_for %in% injury_gwas]
print("Percentage of GWAS traits not accounted for so far")[1] "Percentage of GWAS traits not accounted for so far"round(100 * length(not_accounted_for) / length(all_gwas_terms),
digits = 1)[1] 3.3print("Number of GWAS traits not accounted for so far")[1] "Number of GWAS traits not accounted for so far"length(not_accounted_for)[1] 744phenotype <- readLines(here::here("output/trait_ontology/efo_0000651_descendants.txt"))
phenotype = stringr::str_trim(tolower(phenotype))
phenotype_gwas = not_accounted_for[not_accounted_for %in% phenotype]
print("Percentage of GWAS traits under phenotype terms")[1] "Percentage of GWAS traits under phenotype terms"round(100 * length(phenotype_gwas) / length(all_gwas_terms),
digits = 1)[1] 0.2not_accounted_for = not_accounted_for[!not_accounted_for %in% phenotype_gwas]
print("Percentage of GWAS traits not accounted for so far")[1] "Percentage of GWAS traits not accounted for so far"round(100 * length(not_accounted_for) / length(all_gwas_terms),
digits = 1)[1] 3print("Number of GWAS traits not accounted for so far")[1] "Number of GWAS traits not accounted for so far"length(not_accounted_for)[1] 695gwas_study_info =
gwas_study_info |>
dplyr::mutate(MAPPED_TRAIT_CATEGORY = dplyr::case_when(MAPPED_TRAIT %in% disease_gwas ~ "Disease/Disorder",
MAPPED_TRAIT %in% pheno_abnorm_gwas ~ "Phenotypic Abornmality",
MAPPED_TRAIT %in% measurement_gwas ~ "Measurement",
MAPPED_TRAIT %in% response_gwas ~ "Response",
TRUE ~ "Other"
)
)gwas_study_info$MAPPED_BACKGROUND_TRAIT |> unique() -> gwas_background
gwas_background = stringr::str_trim(tolower(gwas_background))multiple_terms = grep(",", gwas_background, value = T)
mask <- Reduce(`|`, lapply(disease_terms, function(x) grepl(x, multiple_terms)))
additional_disease_gwas <- multiple_terms[mask]
disease_gwas = c(gwas_background[gwas_background %in% disease_terms],
additional_disease_gwas)gwas_study_info <-
gwas_study_info |>
rowwise() |>
dplyr::mutate(
background_disease_terms =
ifelse(MAPPED_BACKGROUND_TRAIT %in% disease_gwas,
find_disease_terms(MAPPED_BACKGROUND_TRAIT),
NA)
)not_accounted_background = gwas_background[!gwas_background %in% disease_gwas]
measurement_gwas <- not_disease_terms[
sapply(strsplit(not_accounted_background, ", "), function(parts) {
parts <- trimws(parts) # remove extra spaces
all(parts %in% measurement)
})
]
measurement_gwas = c(measurement_gwas, additional_measurement) |> unique()
additional_measurement <- not_accounted_background[not_accounted_background %in% measurement]not_accounted_background = not_accounted_background[!not_accounted_background %in% measurement_gwas]
response_gwas = not_accounted_background[not_accounted_background %in% response]
gwas_study_info =
gwas_study_info |>
dplyr::mutate(BACKGROUND_TRAIT_CATEGORY = dplyr::case_when(MAPPED_BACKGROUND_TRAIT %in% disease_gwas ~ "Disease/Disorder",
MAPPED_BACKGROUND_TRAIT %in% measurement_gwas ~ "Measurement",
MAPPED_BACKGROUND_TRAIT %in% response_gwas ~ "Response",
TRUE ~ "Other"
))gwas_study_info |>
group_by(MAPPED_TRAIT_CATEGORY, BACKGROUND_TRAIT_CATEGORY) |>
summarise(n_studies = n()) |>
arrange(desc(n_studies))# A tibble: 18 × 3
# Groups: MAPPED_TRAIT_CATEGORY [5]
MAPPED_TRAIT_CATEGORY BACKGROUND_TRAIT_CATEGORY n_studies
<chr> <chr> <int>
1 Measurement Measurement 84977
2 Other Measurement 27173
3 Disease/Disorder Measurement 16585
4 Measurement Disease/Disorder 7252
5 Other Disease/Disorder 5109
6 Phenotypic Abornmality Measurement 436
7 Disease/Disorder Disease/Disorder 365
8 Response Measurement 274
9 Measurement Other 256
10 Response Disease/Disorder 155
11 Other Other 108
12 Disease/Disorder Other 97
13 Phenotypic Abornmality Disease/Disorder 37
14 Response Other 13
15 Phenotypic Abornmality Other 11
16 Measurement Response 5
17 Disease/Disorder Response 1
18 Other Response 1gwas_study_info =
gwas_study_info |>
dplyr::rowwise() |>
dplyr::mutate(DISEASE_STUDY = ifelse(MAPPED_TRAIT_CATEGORY == "Disease/Disorder" | BACKGROUND_TRAIT_CATEGORY == "Disease/Disorer", T, F )) |>
dplyr::ungroup()combined_disease_terms = function(MAPPED_TRAIT_1, MAPPED_TRAIT_2){
MAPPED_TRAIT_1 = stringr::str_split(MAPPED_TRAIT_1, ", ") |> unlist()
MAPPED_TRAIT_2 = stringr::str_split(MAPPED_TRAIT_2, ", ") |> unlist()
all_mapped_disease_terms =
c(MAPPED_TRAIT_1, MAPPED_TRAIT_2) |>
unique()
combined_mapped_disease_terms = paste0(all_mapped_disease_terms,
collapse = ", ")
return(combined_mapped_disease_terms)
}
gwas_study_info <-
gwas_study_info |>
dplyr::rowwise() |>
dplyr::mutate(all_disease_terms =
case_when(is.na(background_disease_terms) & is.na(disease_terms) ~ NA,
is.na(background_disease_terms) & !is.na(disease_terms) ~ disease_terms,
!is.na(background_disease_terms) & is.na(disease_terms) ~ background_disease_terms,
!is.na(background_disease_terms) & !is.na(disease_terms) ~
combined_disease_terms(background_disease_terms,
disease_terms))
) |>
dplyr::ungroup()data.table::fwrite(gwas_study_info,
here::here("output/gwas_study_info_trait_ontology_info.csv"),
sep = ",")
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] dplyr_1.1.4 data.table_1.17.8 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] utf8_1.2.6 cachem_1.1.0 stringi_1.8.7 httpuv_1.6.16
[29] xfun_0.52 getPass_0.2-4 fs_1.6.6 sass_0.4.10
[33] cli_3.6.5 withr_3.0.2 magrittr_2.0.3 ps_1.9.1
[37] grid_4.3.1 digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1
[41] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.4 glue_1.8.0
[45] farver_2.1.2 whisker_0.4.1 rmarkdown_2.29 tools_4.3.1
[49] pkgconfig_2.0.3 htmltools_0.5.8.1