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| Rmd | b209d1f | IJbeasley | 2025-09-05 | Even more trait collapsing |
library(dplyr)
library(data.table)
library(ggplot2)
library(stringr)gwas_study_info <- fread(here::here("output/gwas_study_info_trait_ontology_info.csv"))Let’s look at the number of studies associated with each unique disease/trait term before any grouping or collapsing.
n_studies_trait = gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(all_disease_terms, PUBMED_ID) |>
dplyr::distinct() |>
dplyr::group_by(all_disease_terms) |>
dplyr::summarise(n_studies = dplyr::n()) |>
dplyr::arrange(desc(n_studies))
head(n_studies_trait)# A tibble: 6 × 2
all_disease_terms n_studies
<chr> <int>
1 , type 2 diabetes mellitus 125
2 , alzheimer disease 95
3 , major depressive disorder 85
4 , breast carcinoma 84
5 , colorectal cancer 84
6 , schizophrenia 83dim(n_studies_trait)[1] 3385 2# Basic cleaning of disease terms
# Removes trailing commas,
gwas_study_info$all_disease_terms = sub(",$", "", gwas_study_info$all_disease_terms)
# trims whitespace
gwas_study_info$all_disease_terms = stringr::str_trim(gwas_study_info$all_disease_terms)
# remove apostrophes
gwas_study_info$all_disease_terms = stringr::str_remove_all(gwas_study_info$all_disease_terms, "'|’")
# initializes a new column (collected_all_disease_terms) to standardized traits
# collapse more traits
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms = all_disease_terms) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"^susceptibility to (.*?) measurement$", "\\1")
) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"^susceptibility to (.*?) (.*?) measurement$", "\\1")
) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"^susceptibility to (.*?) (.*?) infection$", "\\1")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"susceptibility to viral and mycobacterial infections",
"viral and mycobacterial infections")
) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"susceptibility to strep throat",
"strep throat")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove(collected_all_disease_terms, " symptom severity measurement")
) |>
mutate(collected_all_disease_terms =
stringr::str_remove(collected_all_disease_terms, " severity measurement| exacerbation measurement")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\bdependence\\s+measurement\\b",
"dependence")) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\ballergy\\s+measurement\\b",
"allergy")) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\baddiction\\s+measurement\\b",
"addiction")) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\bsyndrome\\s+measurement\\b",
"syndrome")) |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"\\bdisorder\\s+measurement\\b",
"disorder")) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove(collected_all_disease_terms,
pattern = "age of onset of "))
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms ,
pattern = "age of onset of type 2 diabetes mellitus",
"type 2 diabetes mellitus"
)
)
gwas_study_info =
gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms ,
pattern = "age of onset of alzheimer disease",
"alzheimers disease"
)
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_remove(collected_all_disease_terms,
pattern = "family history of "))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"family history of alzheimer’s disease",
"alzheimers disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"time to remission of covid-19 symptoms",
"covid-19"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"adhd symptom measurement",
"adhd")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"agoraphobia symptom measurement",
"agoraphobia"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"alzheimer disease neuropathological change",
"alzheimers disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"asthma exacerbation measurement",
"asthma"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"asthma symptoms measurement",
"asthma"
)) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"covid-19 symptoms measurement",
"covid-19")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"irritable bowel syndrome symptom measurement",
"irritable bowel syndrome"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"parkinsons disease symptom measurement",
"parkinsons disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"post-traumatic stress disorder symptom measurement",
"post-traumatic stress disorder"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"respiratory symptom change measurement" ,
"respiratory symptom measurement"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"anxiety disorder measurement",
"anxiety disorder"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"coronary atherosclerosis measurement",
"coronary atherosclerosis")
) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"insomnia measurement",
"insomnia"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"lewy body dementia measurement",
"lewy body dementia"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"psychosis predisposition measurement",
"psychosis predisposition")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"sleep apnea measurement",
"sleep apnea"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
str_replace_all(collected_all_disease_terms,
"susceptibility to infectious disease measurement",
"susceptibility to infectious disease")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"alcohol dependence measurement",
"alcohol dependence"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"cannabis dependence measurement",
"cannabis dependence"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"cocaine use disorder|cocaine dependence",
"cocaine-related disorders"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"nicotine dependence symptom count",
"nicotine dependence"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"nicotine withdrawal symptom count|nicotine withdrawal measurement",
"nicotine withdrawal"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"\\bcarcinoma",
"cancer")
)
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"triple-negative breast cancer",
"breast cancer"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"coronary atherosclerosis",
"coronary artery disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"head and neck malignant neoplasia",
"head and neck cancer"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"hepatitis a virus infection",
"hepatitis a infection"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"hepatitis b virus infection",
"hepatitis b infection"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"hepatitis c virus infection",
"hepatitis c infection"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"chronic hepatitis c virus infection",
"chronic hepatitis, hepatitis c infection"
)) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"chronic hepatitis b virus infection",
"chronic hepatitis, hepatitis b infection"
))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"hepatitis virus-related liver cancer",
"hepatitis, liver cancer"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"hiv-1 infection",
"hiv infection"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"mumps virus infectious disease",
"mumps"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"renal cancer",
"kidney cancer"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"rubella infection",
"rubella"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"multiple sclerosis symptom measurement",
"multiple sclerosis"
)) gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"autism spectrum disorder",
"autism")
) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"asperger syndrome",
"autism")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"type 1 diabetes mellitus",
"type 1 diabetes")
) |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"type 1 diabetes",
"type 1 diabetes mellitus")
)gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"attention deficit hyperactivity disorder",
"adhd"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"narcolepsy without cataplexy",
"narcolepsy"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"alzheimer disease",
"alzheimers disease"
))gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms =
stringr::str_replace_all(collected_all_disease_terms,
"parkinson disease",
"parkinsons disease"
))gwas_study_info = gwas_study_info |>
rowwise() |>
mutate(
collected_all_disease_terms = paste0(
unique(unlist(stringr::str_split(collected_all_disease_terms, ", "))),
collapse = ", "
)
) |>
ungroup()
gwas_study_info$collected_all_disease_terms = stringr::str_trim(gwas_study_info$collected_all_disease_terms)
gwas_study_info$collected_all_disease_terms = sub(",$", "", gwas_study_info$collected_all_disease_terms)
gwas_study_info$collected_all_disease_terms = stringr::str_replace_all(gwas_study_info$collected_all_disease_terms, "^, ", "")n_studies_trait = gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(collected_all_disease_terms, PUBMED_ID) |>
dplyr::distinct() |>
dplyr::group_by(collected_all_disease_terms) |>
dplyr::summarise(n_studies = dplyr::n()) |>
dplyr::arrange(desc(n_studies))
head(n_studies_trait)# A tibble: 6 × 2
collected_all_disease_terms n_studies
<chr> <int>
1 type 2 diabetes mellitus 145
2 alzheimers disease 114
3 breast cancer 113
4 asthma 110
5 major depressive disorder 108
6 schizophrenia 103dim(n_studies_trait)[1] 3091 2diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms) |>
unlist() |>
stringr::str_trim()
length(unique(diseases))[1] 2204gwas_study_info <- fwrite(gwas_study_info,
here::here("output/gwas_study_info_trait_ontology_info.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] stringr_1.5.1 ggplot2_3.5.2 data.table_1.17.8 dplyr_1.1.4
[5] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 jsonlite_2.0.0 compiler_4.3.1 renv_1.0.3
[5] promises_1.3.3 tidyselect_1.2.1 Rcpp_1.1.0 git2r_0.36.2
[9] callr_3.7.6 later_1.4.2 jquerylib_0.1.4 scales_1.4.0
[13] yaml_2.3.10 fastmap_1.2.0 here_1.0.1 R6_2.6.1
[17] generics_0.1.4 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 httr_1.4.7
[49] tools_4.3.1 pkgconfig_2.0.3 htmltools_0.5.8.1