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library(dplyr)
library(stringr)
library(data.table)source(here::here("code/get_term_descendants.R"))gwas_study_info <- fread(here::here("output/gwas_cat/gwas_study_info_group_v2.csv"))
gwas_study_info = gwas_study_info |>
mutate(collected_all_disease_terms = stringi::stri_trans_general(collected_all_disease_terms, "Latin-ASCII")
)disease_mapping <- gwas_study_info |>
filter(DISEASE_STUDY == T) |>
filter(collected_all_disease_terms != " ") |>
filter(collected_all_disease_terms != "") |>
tidyr::separate_longer_delim(cols = collected_all_disease_terms,
delim = ", ") |>
select(`DISEASE/TRAIT`,
collected_all_disease_terms,
PUBMED_ID) |>
distinct()
print("Number of unique disease trait & study pairs")[1] "Number of unique disease trait & study pairs"nrow(disease_mapping)[1] 37378diseases <- stringr::str_split(pattern = ", ",
gwas_study_info$collected_all_disease_terms[gwas_study_info$collected_all_disease_terms != ""]) |>
unlist() |>
stringr::str_trim()
diseases <- unique(diseases)
print("Number of unique disease terms")[1] "Number of unique disease terms"print(length(diseases))[1] 1687disease_mapping <- disease_mapping |>
mutate(
phecode = str_extract(`DISEASE/TRAIT`, "(?<=PheCode )[^)]+")
) |>
mutate(phecode = as.numeric(phecode))# phecode to ICD10 mapping from https://wei-lab.app.vumc.org/phecode-data/phecode_international_version
phecodes <- fread(here::here("data/icd/phecode_international_version_unrolled.csv"))
phecode_icd_map =
phecodes |>
select(icd10_code = ICD10,
phecode = PheCode
)
# if more than one ICD10 code per phecode, collapse into a single row
phecode_icd_map =
phecode_icd_map |>
group_by(phecode) |>
summarise(icd10_code =
str_flatten(unique(icd10_code), collapse = ", ", na.rm = T),
.groups = "drop")
# phecode icd 10 map
phecode_icd_map =
phecode_icd_map |>
mutate(icd10_code_origin = "Study PheCode Mapping")
disease_mapping =
left_join(disease_mapping,
phecode_icd_map,
by = "phecode",
relationship = "many-to-one",
na_matches = "never")
# disease_mapping =
# disease_mapping |>
# mutate(icd10_code_origin = "Study PheCode")
disease_mapping |>
filter(!is.na(icd10_code_origin)) |>
nrow()[1] 3273disease_mapping |>
filter(!is.na(icd10_code_origin)) |>
head() DISEASE/TRAIT
1 Neurofibromatosis (PheCode 199.4)
2 Myeloproliferative disease (PheCode 200)
3 Polycythemia vera (PheCode 200.1)
4 Hodgkin's disease (PheCode 201)
5 Cancer of other lymphoid, histiocytic tissue (PheCode 202)
6 Non-Hodgkins lymphoma (PheCode 202.2)
collected_all_disease_terms PUBMED_ID phecode
1 neurofibromatosis 30104761 199.4
2 myeloproliferative disorder 30104761 200.0
3 polycythemia vera 30104761 200.1
4 hodgkins lymphoma 30104761 201.0
5 lymphatic system cancer 30104761 202.0
6 non-hodgkins lymphoma 30104761 202.2
icd10_code
1 Q85.0
2 C88.7, C94.4, C94.5, D46, D46.0, D46.1, D46.2, D46.4, D46.7, D46.9, D47.0, D47.1, D47.3, D47.7, D47.9, D57.8, D75.2
3 D45
4 C81, C81.0, C81.1, C81.2, C81.3, C81.7, C81.9
5 C96.0, C96.1, C96.2, C96.3, Z85.7
6 B21.1, C82.0, C82.1, C82.2, C82.7, C83, C83.0, C83.1, C83.2, C83.4, C83.5, C83.6, C83.7, C83.8, C83.9, C84, C84.0, C84.1, C84.2, C84.3, C84.4, C84.5, C85, C85.1, C85.7, C85.9, C96.7, C96.9, L41.2
icd10_code_origin
1 Study PheCode Mapping
2 Study PheCode Mapping
3 Study PheCode Mapping
4 Study PheCode Mapping
5 Study PheCode Mapping
6 Study PheCode Mappingdisease_mapping |>
filter(is.na(icd10_code) & !is.na(phecode)) |>
nrow()[1] 316phecode = c("38.30",
"79.90",
"110.00",
"530.13",
"562.20",
"580.10",
"174.00",
"174.20",
"189.10",
"218.00",
"228.10",
"224.00",
"250.15",
"250.25",
"250.40",
"285.21",
"292.11",
"362.26",
"362.23",
"362.27",
"362.50",
"452.20",
"528.10",
"535.90",
"724.10",
"724.22",
"740.00",
"743.10",
"743.12",
"743.13",
"172.21",
"274.00",
"286.00",
"282.00",
"280.00",
"272.00",
"276.00",
"338.00",
"350.00",
"401.00",
"411.00",
"414.20",
"415.1",
"427.21",
"429.00",
"585.00",
"735.22",
"724.00",
"722.00",
"716.10",
"709.00",
"706.00",
"592.00",
"571.00",
"580.00",
"170.00",
"172.00",
"264.00",
"291.00",
"555.00",
"562.00",
"578.00")
icd10_code = c("A49.9",
"B34.9",
"B35, B36",
"K22.7",
"K57",
"N00, N01, N02, N03, N04, N05, N06, N07",
"Z85.3",
"C50",
"C64, C65",
"D25, D26",
"D18.0",
"E00, E00.0, E00.1, E00.2, E00.9, E01.8, E02, E03.0, E03.1, E03.2, E03.3, E03.8, E03.9, E89.0",
"E10.5",
"E11.5",
"R73.0",
"D63",
"R47.0",
"H35.3",
"H35.3",
"H35.3",
"H35.5",
"I80",
"K12.30",
"K29.7, K29.8, K29.9",
"M43.2",
"M21.5",
"M13.9, M15.0, M15.1, M15.2, M15.3, M15.4, M16, M16.0, M16.1, M16.3, M16.6, M16.7, M16.9, M17.1, M17.4, M17.5, M18.0, M18.1, M18.5, M18.9, M19.0, M19.2",
"M81",
"M81.8",
"M81.8",
"C44",
"M10, M10.0, M10.1, M10.2, M10.4, M10.9, M11.0, M11.1, M11.2, M11.8, M11.9, M67.9",
"D65, D66, D67, D68, D68, D68.0, D68.1, D68.2, D68.3, D68.4, D68.8, D68.9, O72.3, O99.1",
"D55, D55.0, D55.1, D55.2, D55.3, D55.8, D55.9, D56, D56.0, D56.1, D56.2, D56.3, D56.4, D56.8, D56.9, D57, D57.0, D57.1, D57.2, D57.3, D57.8, D58, D58.0, D58.1, D58.2, D58.8, D58.9, M90.4",
"D50, D50.0, D50.1, D50.8, D50.9",
"E78.0, E78.1, E78.2, E78.3, E78.4, E78.5, E78.9",
"E86, E87.0, E87.1, E87.2, E87.3, E87.4, E87.5, E87.6, E87.7, E87.8, R63.1",
"R52.0, R52.2, R52.9",
"R25, R25.0, R25.1, R25.2, R25.3, R25.8, R26, R26.0, R26.1, R26.8, R27, R27.0, R27.8, R29.0, R29.2, R43, R43.0, R43.1, R43.2",
"I10, I11, I11.0, I11.9, I12, I12.0, I12.9, I13, I13.0, I13.1, I13.2, I13.9, I15, I15.0, I15.1, I15.2, I15.8, I15.9, I67.4",
"I20, I20.0, I20.1, I20.8, I20.9, I21, I21.0, I21.1, I21.2, I21.3, I21.4, I21.9, I22, I22.0, I22.1, I22.8, I22.9, I23, I23.0, I23.1, I23.2, I23.3, I23.6, I23.8, I24, I24.0, I24.1, I24.8, I24.9, I25, I25.1, I25.2, I25.3, I25.4, I25.5, I25.6, I25.8, I25.9, I34.1, I51.0, I51.3, Z95.1, Z95.5",
"I25.10",
"I26, I26.0",
"I48",
"I51.8",
"N17, N17.0, N17.1, N17.2, N17.8, N17.9, N18, N18.0, N18.9, N19, Y60.2, Y61.2, Y62.0, Y84.1, Z49.1, Z49.2, Z99.2",
"M21.5",
"M40.2, M43.2, M43.8, M48.8, M49.8, M50.0, M99.6",
"G55.1, M46.4, M50, M50.0, M50.0, M50.1, M50.2, M50.3, M50.8, M50.9, M51.3, M51.4, M96.1",
"M13.0",
"L94.3, M33, M33.0, M33.1, M33.2, M33.9, M34, M34.0, M34.1, M34.2, M34.8, M34.9, M35.0, M35.1, M35.5, M35.8, M35.9, M36.0, M36.8, M65.3, N16.4",
"K09.8, L70, L70.0, L70.1, L70.2, L70.3, L70.4, L70.5, L70.8, L70.9, L72, L72.0, L72.1, L72.2, L72.8, L72.9, L73.0, L85.3",
"N30, N30.0, N30.1, N30.2, N30.3, N30.8, N30.9, N34, N34.0, N34.2, N34.3, N35.1, N37",
"K70.4, K72, K72.1, K72.9, K74.0, K74.1, K74.2, K74.3, K74.4, K74.5, K74.6, K75.0, K75.1, K76.0, K76.6, K76.7",
"B52.0, N00.0, N00.1, N00.2, N00.3, N00.4, N00.5, N00.6, N00.7, N01, N01.0, N01.1, N01.2, N01.3, N01.4, N01.5, N01.6, N01.7, N01.9, N02.0, N02.1, N02.2, N02.3, N02.4, N02.5, N02.6, N02.7, N03, N03.0, N03.1, N03.2, N03.3, N03.4, N03.5, N03.6, N03.7, N03.9, N04, N04.0, N04.1, N04.2, N04.3, N04.4, N04.5, N04.6, N04.7, N04.8, N04.9, N05, N05.0, N05.1, N05.2, N05.3, N05.4, N05.5, N05.6, N05.7, N05.9, N06.0, N06.1, N06.2, N06.3, N06.4, N06.5, N06.6, N06.7, N07.0, N07.1, N07.2, N07.3, N07.4, N07.5, N07.6, N07.7, N08, N08.1, N08.2, N08.3, N08.4, N08.5, N08.8, N14, N14.0, N14.1, N14.2, N14.3, N14.4, N15.0, N15.8, N16.1, N16.2, N16.3, N16.4, N16.5",
"C40, C40.0, C40.1, C40.2, C40.3, C40.8, C40.9, C41, C41.0, C41.1, C41.2, C41.3, C41.4, C41.9, C47, C47.0, C47.1, C47.2, C47.3, C47.4, C47.5, C47.6, C47.8, C47.9, C49, C49.0, C49.1, C49.2, C49.3, C49.4, C49.5, C49.6, C49.8, C49.9",
"C43, C43.0, C43.1, C43.2, C43.3, C43.4, C43.5, C43.6, C43.7, C43.8, C43.9, C44.0, C44.1, C44.2, C44.3, C44.4, C44.5, C44.6, C44.7, C44.8, C44.9, D03, D03.0, D03.1, D03.2, D03.3, D03.4, D03.5, D03.6, D03.7, D03.8, D03.9, D04, D04.0, D04.1, D04.2, D04.3, D04.4, D04.5, D04.6, D04.7, D04.8, D04.9",
"R62.0, R62.8, R62.9",
"F06, F06.1, F07.0, F07.1, F07.2, F07.8, F07.9, F23, F23.0, F23.1, F23.8, F23.9, G47.1, R40.0, R40.1",
"K50, K50.0, K50.1, K50.8, K50.9, K51, K51.0, K51.1, K51.2, K51.3, K51.4, K51.5, K51.8, K51.9",
"K57, K57.0, K57.1, K57.2, K57.3, K57.4, K57.5, K57.8, K57.9",
"K62.5, K92.0, K92.1, K92.2")
icd10_code_origin = rep("Study PheCode (Manual Mapping)",
length(phecode))
to_add = data.frame(phecode,
icd10_code,
icd10_code_origin)
to_add =
to_add |>
mutate(phecode = as.numeric(phecode))
disease_mapping =
rows_patch(disease_mapping,
to_add,
unmatched = "ignore")Matching, by = "phecode"phenotype_icd_map =
phecodes |>
group_by(Phenotype) |>
summarise(icd10_code =
str_flatten(ICD10, collapse = ", ", na.rm = T),
.groups = "drop")
matched_phenotypes =
phenotype_icd_map #|>
#filter(tolower(Phenotype) %in% not_found_diseases)
matched_phenotypes =
matched_phenotypes |>
mutate(collected_all_disease_terms = tolower(Phenotype)) |>
select(collected_all_disease_terms, icd10_code) |>
mutate(icd10_code_origin = "Phecode Phenotype Match")
# match by collected_all_disease_terms
disease_mapping =
disease_mapping |>
rows_patch(matched_phenotypes,
unmatched = "ignore")
# match by DISEASE/TRAIT
matched_phenotypes =
matched_phenotypes |>
rename(`DISEASE/TRAIT` = collected_all_disease_terms)
disease_mapping =
disease_mapping |>
rows_patch(matched_phenotypes,
unmatched = "ignore")
disease_mapping |>
filter(icd10_code_origin == "Phecode Phenotype Match") |>
nrow()[1] 4596# disease_mapping =
# disease_mapping |>
# filter(icd10_code != "")
matched <- c(disease_mapping_matched$collected_all_disease_terms,
matched_phenotypes$collected_all_disease_terms)Warning: Unknown or uninitialised column: `collected_all_disease_terms`.not_found_diseases <- diseases[!diseases %in%
matched
]
not_found_diseases <- not_found_diseases[not_found_diseases != ""]
print(length(not_found_diseases))[1] 459matched_icd10_desc =
phecodes |>
#filter(tolower(iconv(ICD_DESCRIPTION, to = "UTF-8")) %in% not_found_diseases) |>
mutate(collected_all_disease_terms = tolower(iconv(ICD_DESCRIPTION, to = "UTF-8"))) |>
select(collected_all_disease_terms,
icd10_code = ICD10)
matched_icd10_desc =
matched_icd10_desc |>
group_by(collected_all_disease_terms) |>
summarise(icd10_code = str_flatten(unique(icd10_code),
collapse = ", ",
na.rm = T),
.groups = "drop")
# match by collected_all_disease_terms
matched_icd10_desc =
matched_icd10_desc |>
mutate(icd10_code_origin = "ICD Description Match")
disease_mapping =
disease_mapping |>
rows_patch(matched_icd10_desc,
unmatched = "ignore")
# match by DISEASE/TRAIT
matched_icd10_desc =
matched_icd10_desc |>
rename(`DISEASE/TRAIT` = collected_all_disease_terms)
disease_mapping =
rows_patch(disease_mapping,
matched_icd10_desc,
unmatched = "ignore")
disease_mapping |>
filter(icd10_code_origin == "ICD Description Match") |>
nrow()[1] 12161# disease_mapping =
# disease_mapping |>
# filter(icd10_code != "")
matched <- c(disease_mapping_matched$collected_all_disease_terms,
matched_phenotypes$collected_all_disease_terms,
to_add$collected_all_disease_terms)Warning: Unknown or uninitialised column: `collected_all_disease_terms`.not_found_diseases <- diseases[!diseases %in% matched]
not_found_diseases <- not_found_diseases[not_found_diseases != ""]
print(length(not_found_diseases))[1] 459disease_mapping |>
filter(is.na(icd10_code_origin)) |>
nrow()[1] 13674manual_icd10_map <-
readxl::read_xlsx(here::here("data/icd/manual_disease_icd10_mappings.xlsx"))
manual_icd10_map =
manual_icd10_map |>
select(collected_all_disease_terms = mapped_trait,
icd10_code) |>
mutate(icd10_code_origin = "Manual Mapping (collected_all_disease_terms)")
# disease_mapping =
# bind_rows(disease_mapping, to_add) |>
# distinct()
disease_mapping =
rows_patch(disease_mapping,
manual_icd10_map,
unmatched = "ignore")Matching, by = "collected_all_disease_terms"disease_mapping |>
filter(icd10_code_origin == "Manual Mapping (collected_all_disease_terms)") |>
nrow()[1] 1194# disease_mapping =
# disease_mapping |>
# filter(icd10_code != "")
matched <- c(disease_mapping_matched$collected_all_disease_terms,
matched_phenotypes$collected_all_disease_terms,
to_add$collected_all_disease_terms,
manual_icd10_map$collected_all_disease_terms)Warning: Unknown or uninitialised column: `collected_all_disease_terms`.not_found_diseases <- diseases[!diseases %in% matched]
not_found_diseases <- not_found_diseases[not_found_diseases != ""]
print(length(not_found_diseases))[1] 133# similar studies:
study_icd_map =
disease_mapping |>
filter(!is.na(icd10_code)) |>
filter(icd10_code_origin == "Study Provided" | icd10_code_origin == "Study PheCode Mapping")
study_icd_map =
study_icd_map |>
select(collected_all_disease_terms, icd10_code) |>
distinct()
study_icd_map =
study_icd_map |>
group_by(collected_all_disease_terms) |>
summarise(icd10_code = str_flatten(unique(sort(icd10_code)),
collapse = ", ",
na.rm = T),
.groups = "drop")
study_icd_map =
study_icd_map |>
mutate(icd10_code_origin = "Inferred from similar studies")
disease_mapping =
rows_patch(disease_mapping,
study_icd_map,
unmatched = "ignore")Matching, by = "collected_all_disease_terms"disease_mapping |>
filter(!is.na(icd10_code)) |> filter(collected_all_disease_terms == "adhd") DISEASE/TRAIT
1 Attention deficit hyperactivity disorder and obsessive compulsive disorder
2 Attention deficit hyperactivity disorder or cannabis use
3 Attention deficit hyperactivity disorder
4 Response to methylphenidate treatment in attention-deficit/hyperactivity disorder
5 Attention deficit hyperactivity disorder
6 Oppositional defiant disorder dimensions in attention-deficit hyperactivity disorder
7 Attention function in attention deficit hyperactive disorder
8 Aggressiveness in attention deficit hyperactivity disorder
9 Oppositional defiant disorder dimensions in attention-deficit hyperactivity disorder
10 Attention deficit hyperactivity disorder
11 Attention deficit hyperactivity disorder symptoms (maternal expressed emotions interaction)
12 Attention deficit hyperactivity disorder and conduct disorder
13 Attention deficit hyperactivity disorder
14 Attention deficit hyperactivity disorder (combined symptoms)
15 Attention deficit hyperactivity disorder (hyperactivity-impulsivity symptoms)
16 Attention deficit hyperactivity disorder (inattention symptoms)
17 Attention deficit hyperactivity disorder
18 Attention deficit hyperactivity disorder (time to onset)
19 Attention deficit hyperactivity disorder
20 Attention deficit hyperactivity disorder motor coordination
21 Attention deficit hyperactivity disorder
22 Attention deficit hyperactivity disorder
23 Attention deficit hyperactivity disorder
24 Autism spectrum disorder, attention deficit-hyperactivity disorder, bipolar disorder, major depressive disorder, and schizophrenia (combined)
25 Attention deficit hyperactivity disorder
26 Attention deficit hyperactivity disorder
27 Attention deficit hyperactivity disorder
28 Attention deficit hyperactivity disorder
29 Executive inhibition (Stroop WIT and CIT) in attention deficit hyperactivity disorder
30 Bipolar disorder (age of onset <21) or attention deficit hyperactivity disorder
31 Bipolar disorder or attention deficit hyperactivity disorder
32 Attention deficit hyperactivity disorder (sex interaction)
33 Sex difference in attention deficit hyperactivity disorder
34 Attention deficit hyperactivity disorder
35 Attention deficit hyperactivity disorder or educational attainment (years of education) (pleiotropy)
36 Attention deficit hyperactivity disorder symptom score
37 Attention deficit hyperactivity disorder, intelligence or educational attainment (pleiotropy)
38 Executive function in ADHD
39 Attention deficit hyperactivity disorder
40 Persistent attention-deficit hyperactivity disorder
41 Asthma and attention deficit hyperactivity disorder
42 Mental disorder
43 Psychiatric disorder without cannabis use disorder
44 Irritable bowel syndrome or attention-deficit/hyperactivity disorder (pleiotropy)
45 Peptic ulcer disease or attention-deficit/hyperactivity disorder (pleiotropy)
46 Gastroesophageal reflux disease or attention-deficit/hyperactivity disorder (pleiotropy)
47 Attention deficit hyperactivity disorder
48 Attention deficit hyperactivity disorder (MTAG)
49 Substance uses or psychiatric disorders (pleiotropy)
50 Attention deficit hyperactivity disorder or hippocampal volume (pleiotropy)
51 Attention deficit hyperactivity disorder or nucleus accumbens volume (pleiotropy)
52 Attention deficit hyperactivity disorder or caudate nucleus volume (pleiotropy)
53 Attention deficit hyperactivity disorder or intracranial volume (pleiotropy)
54 Attention deficit hyperactivity disorder or putamen volume (pleiotropy)
55 Attention deficit hyperactivity disorder or amygdala volume (pleiotropy)
56 Attention deficit hyperactivity disorder or pallidum volume (pleiotropy)
57 Attention deficit hyperactivity disorder or thalamus volume (pleiotropy)
58 Attention deficit hyperactivity disorder (ADuLT model adjusted for sex)
59 Attention deficit hyperactivity disorder (ADuLT model)
60 Attention deficit hyperactivity disorder (ADuLT model adjusted for age, sex)
61 Attention deficit hyperactivity disorder (SPACox model adjusted for sex)
62 Attention deficit hyperactivity disorder (adjusted for age, sex)
63 Attention deficit hyperactivity disorder (adjusted for sex)
64 Attention deficit hyperactivity disorder
65 Attention deficit hyperactivity disorder (SPACox model adjusted for age, sex)
66 Attention deficit hyperactivity disorder or risk-taking behavior (pleiotropy)
67 Attention deficit hyperactivity disorder (first diagnosed in adulthood vs childhood)
68 Attention deficit hyperactivity disorder
69 Substance use disorder in attention deficit hyperactivity disorder
70 Autism spectrum disorder in attention deficit hyperactivity disorder
71 Attention deficit hyperactivity disorder first diagnosed in adulthood
72 Attention deficit hyperactivity disorder or Substance use disorder (pleiotropy)
73 Attention deficit hyperactivity disorder or autism spectrum disorder (pleiotropy)
74 Attention deficit hyperactivity disorder and Substance use disorder
75 Attention deficit hyperactivity disorder and Autism spectrum disorder
76 ADHD vs autism spectrum disorder (ordinary least squares (OLS))
77 ADHD vs obsessive compulsive disorder (ordinary least squares (OLS))
78 ADHD vs Tourette's syndrome and other tic disorders (ordinary least squares (OLS))
79 Bipolar disorder vs ADHD (ordinary least squares (OLS))
80 Major depressive disorder vs ADHD (ordinary least squares (OLS))
81 Schizophrenia vs ADHD (ordinary least squares (OLS))
82 ADHD vs anorexia nervosa (ordinary least squares (OLS))
83 Externalizing behaviour (multivariate analysis)
84 Attention deficit hyperactivity disorder
85 Education attainment or attention deficit hyperactivity disorder
86 Attention deficit hyperactivity disorder or autism spectrum disorder (pleiotropy)
87 Type 2 diabetes and Attention deficit hiperactivty disorder or Major depressive disorder or obsessive compulsive disorder
88 Type 2 diabetes and Attention deficit hiperactivty disorder or schyzophrenia or obsessive compulsive disorder
89 Type 2 diabetes and Attention deficit hiperactivty disorder or Anorexia nervosa or Major depressive disorder or schyzophrenia
90 Type 2 diabetes and Attention deficit hiperactivty disorder
91 Type 2 diabetes and Attention deficit hiperactivty disorder or schyzophrenia
92 Type 2 diabetes and Attention deficit hiperactivty disorder or obsessive compulsive disorder
93 Type 2 diabetes and Attention deficit hiperactivty disorder or Anorexia nervosa
94 Type 2 diabetes and Attention deficit hiperactivty disorder or Anorexia nervosa or schyzophrenia
95 Type 2 diabetes and Attention deficit hiperactivty disorder or Anorexia nervosa or Major depressive disorder
96 Type 2 diabetes and Attention deficit hiperactivty disorder or Anorexia nervosa or obsessive compulsive disorder
97 Type 2 diabetes and Attention deficit hiperactivty disorder or Major depressive disorder
98 Type 2 diabetes and Attention deficit hiperactivty disorder or Major depressive disorder or schyzophrenia
99 Type 2 diabetes and Attention deficit hiperactivty disorder or Major depressive disorder or schyzophrenia or obsessive compulsive disorder
100 Type 2 diabetes and Attention deficit hiperactivty disorder or Anorexia nervosa or schyzophrenia or obsessive compulsive disorder
101 Type 2 diabetes and Attention deficit hiperactivty disorder or Anorexia nervosa or Major depressive disorder or obsessive compulsive disorder
102 Type 2 diabetes and Attention deficit hiperactivty disorder or Anorexia nervosa or Major depressive disorder or schyzophrenia or obsessive compulsive disorder
103 Attention deficit hyperactivity disorder (PheCode 313.1)
104 Attention deficit hyperactivity disorder
105 Attention deficit hyperactivity disorder (persistent)
106 Attention deficit hyperactivity disorder (childhood)
107 Attention deficit hyperactivity disorder (MTAG)
108 Neuropsychiatric disorders
109 Attention deficit hyperactivity disorder
110 Attention deficit hyperactivity disorder (inattention symptoms)
111 Attention deficit hyperactivity disorder (hyperactivity-impulsivity symptoms)
112 Attention deficit hyperactivity disorder
113 Disruptive behavior (multivariate analysis)
114 Attention deficit hyperactivity disorder or autism spectrum disorder or intelligence (pleiotropy)
115 Executive inhibition (color interference time) in ADHD
116 Executive inhibition (word interference time) in ADHD
117 Mental disorder
118 Psychiatric diseases (pleiotropy) (HIPO component 1)
119 Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)
120 Attention deficit hyperactivity disorder (inattention symptoms)
121 Emotional lability in attention deficit hyperactivity disorder
122 Attention deficit hyperactivity disorder symptom score
123 Stimulant treatment initiation in ADHD
124 Stimulant treatment discontinuation in ADHD
125 Switch to non-stimulant treatment in ADHD
126 Disruptive behavior disorder in attention deficit hyperactivity disorder
127 Attention deficit hyperactivity disorder
128 Disruptive behavior disorder and attention deficit hyperactivity disorder
129 Attention deficit hyperactivity disorder (childhood)
130 Attention deficit hyperactivity disorder (persistent)
131 Attention deficit hyperactivity disorder (late-diagnosed)
132 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder
133 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Obsesive-compulsive disorder
134 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Schizophrenia
135 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Autism spectrum disorder
136 Obesity class I and Attention deficit hyperactivity disorder or Major depressive disorder or Obsesive-compulsive disorder
137 Obesity class I and Attention deficit hyperactivity disorder or Major depressive disorder or Schizophrenia
138 Obesity class I and Attention deficit hyperactivity disorder or Major depressive disorder or Autism spectrum disorder
139 Obesity class I and Attention deficit hyperactivity disorder or Obsesive-compulsive disorder or Schizophrenia
140 Obesity class I and Attention deficit hyperactivity disorder or Obsesive-compulsive disorder or Autism spectrum disorder
141 Obesity class I and Attention deficit hyperactivity disorder or Schizophrenia or Autism spectrum disorder
142 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Schizophrenia
143 Obesity class II and Attention deficit hyperactivity disorder or Anorexia nervosa
144 Obesity class II and Attention deficit hyperactivity disorder or Schizophrenia
145 Obesity class II and Attention deficit hyperactivity disorder or Major depressive disorder
146 Obesity class II and Attention deficit hyperactivity disorder or Obsesive-compulsive disorder
147 Obesity class I and Attention deficit hyperactivity disorder or Major depressive disorder
148 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa
149 Obesity class I and Attention deficit hyperactivity disorder or Obsesive-compulsive disorder
150 Obesity class I and Attention deficit hyperactivity disorder or Schizophrenia
151 Obesity class I and Attention deficit hyperactivity disorder or Autism spectrum disorder
152 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Obsesive-compulsive disorder
153 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Autism spectrum disorder
154 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Obsesive-compulsive disorder or Schizophrenia
155 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Obsesive-compulsive disorder or Autism spectrum disorder
156 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Schizophrenia or Autism spectrum disorder
157 Obesity class I and Attention deficit hyperactivity disorder or Major depressive disorder or Obsesive-compulsive disorder or Schizophrenia
158 Obesity class I and Attention deficit hyperactivity disorder or Major depressive disorder or Obsesive-compulsive disorder or Autism spectrum disorder
159 Obesity class I and Attention deficit hyperactivity disorder or Major depressive disorder or Schizophrenia or Autism spectrum disorder
160 Obesity class I and Attention deficit hyperactivity disorder or Obsesive-compulsive disorder or Schizophrenia or Autism spectrum disorder
161 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Obsesive-compulsive disorder or Autism spectrum disorder
162 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Obsesive-compulsive disorder or Schizophrenia
163 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Schizophrenia or Autism spectrum disorder
164 Obesity class I and Attention deficit hyperactivity disorder or Major depressive disorder or Obsesive-compulsive disorder or Schizophrenia or Autism spectrum disorder
165 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Obsesive-compulsive disorder or Schizophrenia or Autism spectrum disorder
166 Obesity class I and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Obsesive-compulsive disorder or Schizophrenia or Autism spectrum disorder
167 Obesity class II and attention deficit hyperactivity disorder
168 Obesity class II and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder
169 Obesity class II and Attention deficit hyperactivity disorder or Anorexia nervosa or Obsesive-compulsive disorder
170 Obesity class II and Attention deficit hyperactivity disorder or Major depressive disorder or Obsesive-compulsive disorder
171 Obesity class II and Attention deficit hyperactivity disorder or Anorexia nervosa or Schizophrenia
172 Obesity class II and Attention deficit hyperactivity disorder or Major depressive disorder or Schizophrenia
173 Obesity class II and Attention deficit hyperactivity disorder or Obsesive-compulsive disorder or Schizophrenia
174 Obesity class II and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Obsesive-compulsive disorder
175 Obesity class II and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Schizophrenia
176 Obesity class II and Attention deficit hyperactivity disorder or Anorexia nervosa or Obsesive-compulsive disorder or Schizophrenia
177 Obesity class II and Attention deficit hyperactivity disorder or Major depressive disorder or Obsesive-compulsive disorder or Schizophrenia
178 Obesity class II and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder or Obsesive-compulsive disorder or Schizophrenia
179 Obesity class III and attention deficit hyperactivity disorder
180 Obesity class III and Attention deficit hyperactivity disorder or Anorexia nervosa
181 Obesity class III and Attention deficit hyperactivity disorder or Major depressive disorder
182 Obesity class III and Attention deficit hyperactivity disorder or Anorexia nervosa or Major depressive disorder
183 Obesity class I and Attention deficit hyperactivity disorder
collected_all_disease_terms PUBMED_ID phecode icd10_code
1 adhd 28386217 NA F90, F90.1, F90.9
2 adhd 30610198 NA F90, F90.1, F90.9
3 adhd 28809852 NA F90, F90.1, F90.9
4 adhd 29382897 NA F90, F90.1, F90.9
5 adhd 30478444 NA F90, F90.1, F90.9
6 adhd 26184070 NA F90, F90.1, F90.9
7 adhd 26174813 NA F90, F90.1, F90.9
8 adhd 27021288 NA F90, F90.1, F90.9
9 adhd 27021288 NA F90, F90.1, F90.9
10 adhd 20732626 NA F90, F90.1, F90.9
11 adhd 18846501 NA F90, F90.1, F90.9
12 adhd 18951430 NA F90, F90.1, F90.9
13 adhd 20732627 NA F90, F90.1, F90.9
14 adhd 23527680 NA F90, F90.1, F90.9
15 adhd 23527680 NA F90, F90.1, F90.9
16 adhd 23527680 NA F90, F90.1, F90.9
17 adhd 22420046 NA F90, F90.1, F90.9
18 adhd 18937294 NA F90, F90.1, F90.9
19 adhd 18821565 NA F90, F90.1, F90.9
20 adhd 21473668 NA F90, F90.1, F90.9
21 adhd 18839057 NA F90, F90.1, F90.9
22 adhd 23728934 NA F90, F90.1, F90.9
23 adhd 20732625 NA F90, F90.1, F90.9
24 adhd 23453885 NA F90, F90.1, F90.9
25 adhd 18980221 NA F90, F90.1, F90.9
26 adhd 21784300 NA F90, F90.1, F90.9
27 adhd 22012869 NA F90, F90.1, F90.9
28 adhd 18821564 NA F90, F90.1, F90.9
29 adhd 28416812 NA F90, F90.1, F90.9
30 adhd 27890468 NA F90, F90.1, F90.9
31 adhd 27890468 NA F90, F90.1, F90.9
32 adhd 29325848 NA F90, F90.1, F90.9
33 adhd 29325848 NA F90, F90.1, F90.9
34 adhd 29325848 NA F90, F90.1, F90.9
35 adhd 29413154 NA F90, F90.1, F90.9
36 adhd 27663945 NA F90, F90.1, F90.9
37 adhd 32061372 NA F90, F90.1, F90.9
38 adhd 29769613 NA F90, F90.1, F90.9
39 adhd 25875332 NA F90, F90.1, F90.9
40 adhd 25284319 NA F90, F90.1, F90.9
41 adhd 31619474 NA F90, F90.1, F90.9
42 adhd 31209380 NA F90, F90.1, F90.9
43 adhd 31209380 NA F90, F90.1, F90.9
44 adhd 36753304 NA F90, F90.1, F90.9
45 adhd 36753304 NA F90, F90.1, F90.9
46 adhd 36753304 NA F90, F90.1, F90.9
47 adhd 32606422 NA F90, F90.1, F90.9
48 adhd 32606422 NA F90, F90.1, F90.9
49 adhd 32762793 NA F90, F90.1, F90.9
50 adhd 30818988 NA F90, F90.1, F90.9
51 adhd 30818988 NA F90, F90.1, F90.9
52 adhd 30818988 NA F90, F90.1, F90.9
53 adhd 30818988 NA F90, F90.1, F90.9
54 adhd 30818988 NA F90, F90.1, F90.9
55 adhd 30818988 NA F90, F90.1, F90.9
56 adhd 30818988 NA F90, F90.1, F90.9
57 adhd 30818988 NA F90, F90.1, F90.9
58 adhd 37689771 NA F90, F90.1, F90.9
59 adhd 37689771 NA F90, F90.1, F90.9
60 adhd 37689771 NA F90, F90.1, F90.9
61 adhd 37689771 NA F90, F90.1, F90.9
62 adhd 37689771 NA F90, F90.1, F90.9
63 adhd 37689771 NA F90, F90.1, F90.9
64 adhd 37689771 NA F90, F90.1, F90.9
65 adhd 37689771 NA F90, F90.1, F90.9
66 adhd 38565336 NA F90, F90.1, F90.9
67 adhd 38036780 NA F90, F90.1, F90.9
68 adhd 38036780 NA F90, F90.1, F90.9
69 adhd 38036780 NA F90, F90.1, F90.9
70 adhd 38036780 NA F90, F90.1, F90.9
71 adhd 38036780 NA F90, F90.1, F90.9
72 adhd 38036780 NA F90, F90.1, F90.9
73 adhd 38036780 NA F90, F90.1, F90.9
74 adhd 38036780 NA F90, F90.1, F90.9
75 adhd 38036780 NA F90, F90.1, F90.9
76 adhd 33686288 NA F90, F90.1, F90.9
77 adhd 33686288 NA F90, F90.1, F90.9
78 adhd 33686288 NA F90, F90.1, F90.9
79 adhd 33686288 NA F90, F90.1, F90.9
80 adhd 33686288 NA F90, F90.1, F90.9
81 adhd 33686288 NA F90, F90.1, F90.9
82 adhd 33686288 NA F90, F90.1, F90.9
83 adhd 34446935 NA F90, F90.1, F90.9
84 adhd 37865391 NA F90, F90.1, F90.9
85 adhd 38250258 NA F90, F90.1, F90.9
86 adhd 35717853 NA F90, F90.1, F90.9
87 adhd 36738649 NA F90, F90.1, F90.9
88 adhd 36738649 NA F90, F90.1, F90.9
89 adhd 36738649 NA F90, F90.1, F90.9
90 adhd 36738649 NA F90, F90.1, F90.9
91 adhd 36738649 NA F90, F90.1, F90.9
92 adhd 36738649 NA F90, F90.1, F90.9
93 adhd 36738649 NA F90, F90.1, F90.9
94 adhd 36738649 NA F90, F90.1, F90.9
95 adhd 36738649 NA F90, F90.1, F90.9
96 adhd 36738649 NA F90, F90.1, F90.9
97 adhd 36738649 NA F90, F90.1, F90.9
98 adhd 36738649 NA F90, F90.1, F90.9
99 adhd 36738649 NA F90, F90.1, F90.9
100 adhd 36738649 NA F90, F90.1, F90.9
101 adhd 36738649 NA F90, F90.1, F90.9
102 adhd 36738649 NA F90, F90.1, F90.9
103 adhd 39024449 313.1 F90, F90.1, F90.9
104 adhd 32279069 NA F90, F90.1, F90.9
105 adhd 32279069 NA F90, F90.1, F90.9
106 adhd 32279069 NA F90, F90.1, F90.9
107 adhd 33479212 NA F90, F90.1, F90.9
108 adhd 33479212 NA F90, F90.1, F90.9
109 adhd 30563984 NA F90, F90.1, F90.9
110 adhd 32595297 NA F90, F90.1, F90.9
111 adhd 32595297 NA F90, F90.1, F90.9
112 adhd 32595297 NA F90, F90.1, F90.9
113 adhd 36324656 NA F90, F90.1, F90.9
114 adhd 35764056 NA F90, F90.1, F90.9
115 adhd 38430954 NA F90, F90.1, F90.9
116 adhd 38430954 NA F90, F90.1, F90.9
117 adhd 30692689 NA F90, F90.1, F90.9
118 adhd 30289880 NA F90, F90.1, F90.9
119 adhd 31835028 NA F90, F90.1, F90.9
120 adhd 31959275 NA F90, F90.1, F90.9
121 adhd 31085060 NA F90, F90.1, F90.9
122 adhd 30659475 NA F90, F90.1, F90.9
123 adhd 34154395 NA F90, F90.1, F90.9
124 adhd 34154395 NA F90, F90.1, F90.9
125 adhd 34154395 NA F90, F90.1, F90.9
126 adhd 33495439 NA F90, F90.1, F90.9
127 adhd 33495439 NA F90, F90.1, F90.9
128 adhd 33495439 NA F90, F90.1, F90.9
129 adhd 35927488 NA F90, F90.1, F90.9
130 adhd 35927488 NA F90, F90.1, F90.9
131 adhd 35927488 NA F90, F90.1, F90.9
132 adhd 36137488 NA F90, F90.1, F90.9
133 adhd 36137488 NA F90, F90.1, F90.9
134 adhd 36137488 NA F90, F90.1, F90.9
135 adhd 36137488 NA F90, F90.1, F90.9
136 adhd 36137488 NA F90, F90.1, F90.9
137 adhd 36137488 NA F90, F90.1, F90.9
138 adhd 36137488 NA F90, F90.1, F90.9
139 adhd 36137488 NA F90, F90.1, F90.9
140 adhd 36137488 NA F90, F90.1, F90.9
141 adhd 36137488 NA F90, F90.1, F90.9
142 adhd 36137488 NA F90, F90.1, F90.9
143 adhd 36137488 NA F90, F90.1, F90.9
144 adhd 36137488 NA F90, F90.1, F90.9
145 adhd 36137488 NA F90, F90.1, F90.9
146 adhd 36137488 NA F90, F90.1, F90.9
147 adhd 36137488 NA F90, F90.1, F90.9
148 adhd 36137488 NA F90, F90.1, F90.9
149 adhd 36137488 NA F90, F90.1, F90.9
150 adhd 36137488 NA F90, F90.1, F90.9
151 adhd 36137488 NA F90, F90.1, F90.9
152 adhd 36137488 NA F90, F90.1, F90.9
153 adhd 36137488 NA F90, F90.1, F90.9
154 adhd 36137488 NA F90, F90.1, F90.9
155 adhd 36137488 NA F90, F90.1, F90.9
156 adhd 36137488 NA F90, F90.1, F90.9
157 adhd 36137488 NA F90, F90.1, F90.9
158 adhd 36137488 NA F90, F90.1, F90.9
159 adhd 36137488 NA F90, F90.1, F90.9
160 adhd 36137488 NA F90, F90.1, F90.9
161 adhd 36137488 NA F90, F90.1, F90.9
162 adhd 36137488 NA F90, F90.1, F90.9
163 adhd 36137488 NA F90, F90.1, F90.9
164 adhd 36137488 NA F90, F90.1, F90.9
165 adhd 36137488 NA F90, F90.1, F90.9
166 adhd 36137488 NA F90, F90.1, F90.9
167 adhd 36137488 NA F90, F90.1, F90.9
168 adhd 36137488 NA F90, F90.1, F90.9
169 adhd 36137488 NA F90, F90.1, F90.9
170 adhd 36137488 NA F90, F90.1, F90.9
171 adhd 36137488 NA F90, F90.1, F90.9
172 adhd 36137488 NA F90, F90.1, F90.9
173 adhd 36137488 NA F90, F90.1, F90.9
174 adhd 36137488 NA F90, F90.1, F90.9
175 adhd 36137488 NA F90, F90.1, F90.9
176 adhd 36137488 NA F90, F90.1, F90.9
177 adhd 36137488 NA F90, F90.1, F90.9
178 adhd 36137488 NA F90, F90.1, F90.9
179 adhd 36137488 NA F90, F90.1, F90.9
180 adhd 36137488 NA F90, F90.1, F90.9
181 adhd 36137488 NA F90, F90.1, F90.9
182 adhd 36137488 NA F90, F90.1, F90.9
183 adhd 36137488 NA F90, F90.1, F90.9
icd10_code_origin
1 Inferred from similar studies
2 Inferred from similar studies
3 Inferred from similar studies
4 Inferred from similar studies
5 Inferred from similar studies
6 Inferred from similar studies
7 Inferred from similar studies
8 Inferred from similar studies
9 Inferred from similar studies
10 Inferred from similar studies
11 Inferred from similar studies
12 Inferred from similar studies
13 Inferred from similar studies
14 Inferred from similar studies
15 Inferred from similar studies
16 Inferred from similar studies
17 Inferred from similar studies
18 Inferred from similar studies
19 Inferred from similar studies
20 Inferred from similar studies
21 Inferred from similar studies
22 Inferred from similar studies
23 Inferred from similar studies
24 Inferred from similar studies
25 Inferred from similar studies
26 Inferred from similar studies
27 Inferred from similar studies
28 Inferred from similar studies
29 Inferred from similar studies
30 Inferred from similar studies
31 Inferred from similar studies
32 Inferred from similar studies
33 Inferred from similar studies
34 Inferred from similar studies
35 Inferred from similar studies
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103 Study PheCode Mapping
104 Inferred from similar studies
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182 Inferred from similar studies
183 Inferred from similar studiesicd10_code = c("F90, F90.1, F90.9",
"F00. G30",
"O45",
"H25",
"H25.1")
collected_all_disease_terms = c("adhd",
"alzheimers disease",
"abruptio placentae",
"age-related cataract",
"age-related nuclear cataract")
icd10_code_origin = c("Inferred from similar study")
to_add = data.frame(collected_all_disease_terms,
icd10_code,
icd10_code_origin)
disease_mapping =
rows_patch(disease_mapping,
to_add,
unmatched = "ignore")Matching, by = "collected_all_disease_terms"disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F40 F41 F42",
replacement = "F40, F41, F42"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "G47.8. G47.9",
replacement = "G47.8, G47.9"
)
)disease_mapping =
disease_mapping |>
mutate(icd10_code = str_split(icd10_code, ",\\s*")) |>
tidyr::unnest(icd10_code)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "B37.49",
replacement = "B37.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E05.90",
replacement = "E05.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E11.319|E11.31|E11.329.9|E11.329.|E11.32|E11.3.",
replacement = "E11.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E11.3.",
replacement = "E11.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E13.621.|E13.62",
replacement = "E11.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "E78.00",
replacement = "E78.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F10.10",
replacement = "F10.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F17.201.|F17.20",
replacement = "F17.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "F430",
replacement = "F43.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "G47.00",
replacement = "G47.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H01.00|H01.09.",
replacement = "H01.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H01.09.",
replacement = "H01.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H029",
replacement = "H02.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H60.90",
replacement = "H60.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H60.90",
replacement = "H60.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H91.8X9.",
replacement = "H91.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H91.90",
replacement = "H91.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "H93.299.|H93.29",
replacement = "H01"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "I70.20",
replacement = "I70.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "I82.409.|I82.40|I82.4",
replacement = "I82"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "J30.9",
replacement = "J30.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "J45.998.|J45.909.|J45.901.|J45.99|J45.90",
replacement = "J45.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "J98.457.6",
replacement = "J98.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "K05.30-31",
replacement = "K05.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "K29.70",
replacement = "K29.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "K59.00",
replacement = "K59.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "L08.89",
replacement = "L08.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M06.99|M06.90",
replacement = "M06.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M10.99",
replacement = "M10.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M10.99",
replacement = "M10.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M13.90|M13.94|M13.96|M13.97|M13.99",
replacement = "M13.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M19.07",
replacement = "M19.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M19.90|M19.91|M19.94|M19.97|M19.99",
replacement = "M19.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M25.50|M25.51|M25.55|M25.569.|M25.56|M25.571.|M25.57",
replacement = "M25.5"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M25.76|M25.77",
replacement = "M25.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M43.16",
replacement = "M43.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M47.80|M47.82|M47.86",
replacement = "M47.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M47.92|M47.96",
replacement = "M47.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M48.02|M48.06",
replacement = "M48.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M54.22",
replacement = "M54.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M54.30|M54.39",
replacement = "M54.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M54.56|M54.57|M54.59",
replacement = "M54.5"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M54.99",
replacement = "M54.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M65.34",
replacement = "M65.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M65.96",
replacement = "M65.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M72.04",
replacement = "M72.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M79.09",
replacement = "M79.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M79.65|M79.66|M79.67",
replacement = "M79.6"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M79.79",
replacement = "M79.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M79.86",
replacement = "M79.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "M81.99",
replacement = "M81.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N390",
replacement = "N39.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N50.89",
replacement = "N50.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N52",
replacement = "F52"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N52.9",
replacement = "F52.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "N814",
replacement = "N81.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "P29.12",
replacement = "P29.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R06.00|R06.09",
replacement = "R06.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R06.83",
replacement = "R06.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R07.89",
replacement = "R07.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R07.8|R07.9",
replacement = "R07"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R09.89",
replacement = "R09.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R10.30",
replacement = "R10.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R10.8|R10.9",
replacement = "R10"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R11.0",
replacement = "R11"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R13.10",
replacement = "R13"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R13.1",
replacement = "R13"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R14.0",
replacement = "R14"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R19.7",
replacement = "R19"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R29.898.|R29.89",
replacement = "R29.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R31.29",
replacement = "R31.2"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R31.2|R31.9",
replacement = "R31"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R53.82|R53.83|R5382",
replacement = "R53.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R53.8",
replacement = "R53"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R56.9",
replacement = "R56"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R73.09|R73.02",
replacement = "R73.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R80.9",
replacement = "R80"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R82.998.|R82.99",
replacement = "R82.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R871",
replacement = "R87.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R87.6",
replacement = "R87"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R87.61",
replacement = "R87.6"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T50.905.",
replacement = "T50.9"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T78.40",
replacement = "T78.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T780",
replacement = "T78.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T81.149.88",
replacement = "T81.1"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T81.815.013.",
replacement = "T81.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T84.84",
replacement = "T84.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "T887",
replacement = "T88.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z86.79",
replacement = "Z86.7"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z87.09",
replacement = "Z87.0"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z87.39",
replacement = "Z87.3"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z87.42",
replacement = "Z87.4"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "Z87.891.",
replacement = "Z87.8"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "W44.9",
replacement = "W44"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "U80",
replacement = "U82"
)
)
disease_mapping =
disease_mapping |>
distinct()other_icd10_desc =
data.frame(
icd10_code = c("A09.9",
"A41",
"B95",
"B96",
"B97",
"B98",
"C44",
"C79",
"C80.0",
"C80.9",
"C90",
"D07",
"D35",
"D37",
"D47",
"D48",
"E03",
"E04",
"E21",
"E23",
"E27",
"E61",
"E80",
"E87",
"E89",
"F05",
"F17",
"F41",
"F43.0",
"F53",
"G31",
"G45",
"G46",
"G62",
"G93",
"G99",
"H47",
"H50",
"H57",
"H83",
"H91",
"H92",
"H93",
"I08",
"I27",
"I27.2",
"I44",
"I45",
"I48.0",
"I49",
"I51",
"I62",
"I71",
"J15",
"J16",
"J34",
"J38",
"J69",
"J84",
"J95",
"J96",
"K05",
"K07",
"K08",
"K09",
"K10",
"K12",
"K13",
"K22",
"K22.7",
"K52",
"K56",
"K64",
"K64.0",
"K64.9",
"K74",
"K75",
"K85.9",
"K86",
"K91",
"K91.8",
"K92",
"L02",
"L13",
"L30",
"L65",
"L73",
"L85",
"L89.1",
"L98",
"M05",
"M06",
"M07",
"M11",
"M13",
"M18",
"M19",
"M24",
"M25",
"M31",
"M35",
"M43",
"M48",
"M53",
"M62",
"M66",
"M67",
"M71",
"M77",
"M79",
"M79.7",
"M80",
"M81",
"M85",
"M89",
"M96",
"N02",
"N18.3",
"N18.4",
"N28",
"N39",
"N48",
"N73",
"N76",
"N88",
"N89",
"N91",
"N92",
"N93",
"N94",
"N99",
"O14",
"O04",
"O26",
"O32",
"O34",
"O36",
"O68",
"O75",
"O99",
"R03",
"R07",
"R09",
"R10",
"R19",
"R29",
"R29.6",
"R39",
"R40",
"R47",
"R57",
"T95.8",
"W44",
"Y95",
"Z86.3",
"Z87.3",
"Z87.4",
"Z87.7",
"Z87.8",
"T85.8",
"Z91.0",
"Z88.9",
"Z88.8",
"Z88",
"Z92.6",
"N90",
"U82"
),
icd10_description = c("Gastroenteritis and colitis of unspecified origin",
"Other sepsis",
"Streptococcus and staphylococcus as the cause of diseases classified to other chapters",
"Other specified bacterial agents as the cause of diseases classified to other chapters",
"Viral agents as the cause of diseases classified to other chapters",
"Other specified infectious agents as the cause of diseases classified to other chapters",
"Other malignant neoplasms of skin",
"Secondary malignant neoplasm of other and unspecified sites",
"Malignant neoplasm, primary site unknown, so stated",
"Malignant neoplasm, primary site unspecified",
"Multiple myeloma and malignant plasma cell neoplasms",
"Carcinoma in situ of other and unspecified genital organs",
"Benign neoplasm of other and unspecified endocrine glands",
"Neoplasm of uncertain or unknown behaviour of oral cavity and digestive organs",
"Other neoplasms of uncertain or unknown behaviour of lymphoid, haematopoietic and related tissue",
"Neoplasm of uncertain or unknown behaviour of other and unspecified sites",
"Other hypothyroidism",
"Other nontoxic goitre",
"Hyperparathyroidism and other disorders of parathyroid gland",
"Hypofunction and other disorders of pituitary gland",
"Other disorders of adrenal gland",
"Deficiency of other nutrient elements",
"Disorders of porphyrin and bilirubin metabolism",
"Other disorders of fluid, electrolyte and acid-base balance",
"Postprocedural endocrine and metabolic disorders, not elsewhere classified",
"Delirium, not induced by alcohol and other psychoactive substances",
"Mental and behavioural disorders due to use of tobacco",
"Other anxiety disorders",
"Acute stress reaction",
"Mental and behavioural disorders associated with the puerperium, not elsewhere classified",
"Other degenerative diseases of nervous system, not elsewhere classified",
"Transient cerebral ischaemic attacks and related syndromes",
"Vascular syndromes of brain in cerebrovascular diseases",
"Other polyneuropathies",
"Other disorders of brain",
"Other disorders of nervous system in diseases classified elsewhere",
"Other disorders of optic [2nd] nerve and visual pathways",
"Other strabismus",
"Other disorders of eye and adnexa",
"Other diseases of inner ear",
"Other hearing loss",
"Otalgia and effusion of ear",
"Other disorders of ear, not elsewhere classified",
"Multiple valve diseases",
"Other pulmonary heart diseases",
"Other secondary pulmonary hypertension",
"Atrioventricular and left bundle-branch block",
"Other conduction disorders",
"Paroxysmal atrial fibrillation",
"Ventricular fibrillation and flutter",
"Complications and ill-defined descriptions of heart disease",
"Other nontraumatic intracranial haemorrhage",
"Aortic aneurysm and dissection",
"Bacterial pneumonia, not elsewhere classified",
"Pneumonia due to other infectious organisms, not elsewhere classified",
"Other disorders of nose and nasal sinuses",
"Diseases of vocal cords and larynx, not elsewhere classified",
"Pneumonitis due to solids and liquids",
"Other interstitial pulmonary diseases",
"Postprocedural respiratory disorders, not elsewhere classified",
"Respiratory failure, not elsewhere classified",
"Gingivitis and periodontal diseases",
"Dentofacial anomalies [including malocclusion]",
"Other disorders of teeth and supporting structures",
"Cysts of oral region, not elsewhere classified",
"Other diseases of jaws",
"Stomatitis and related lesions",
"Other diseases of lip and oral mucosa",
"Other diseases of oesophagus",
"Barrett oesophagus",
"Other noninfective gastroenteritis and colitis",
"Paralytic ileus and intestinal obstruction without hernia",
"Haemorrhoids and perianal venous thrombosis",
"First degree haemorrhoids",
"Haemorrhoids, unspecified",
"Fibrosis and cirrhosis of liver",
"Other inflammatory liver diseases",
"Acute pancreatitis, unspecified",
"Other diseases of pancreas",
"Postprocedural disorders of digestive system, not elsewhere classified",
"Other postprocedural disorders of digestive system, not elsewhere classified",
"Other diseases of digestive system",
"Cutaneous abscess, furuncle and carbuncle",
"Other bullous disorders",
"Other dermatitis",
"Other nonscarring hair loss",
"Other follicular disorders",
"Other epidermal thickening",
"Stage II decubitus ulcer",
"Other disorders of skin and subcutaneous tissue, not elsewhere classified",
"Seropositive rheumatoid arthritis",
"Other rheumatoid arthritis",
"Psoriatic and enteropathic arthropathies",
"Other crystal arthropathies",
"Other arthritis",
"Arthrosis of first carpometacarpal joint",
"Other arthrosis",
"Other specific joint derangements",
"Other joint disorders, not elsewhere classified",
"Other necrotizing vasculopathies",
"Other systemic involvement of connective tissue",
"Other deforming dorsopathies",
"Other spondylopathies",
"Other dorsopathies, not elsewhere classified",
"Other disorders of muscle",
"Spontaneous rupture of synovium and tendon",
"Other disorders of synovium and tendon",
"Other bursopathies",
"Other enthesopathies",
"Other soft tissue disorders, not elsewhere classified",
"Fibromyalgia",
"Osteoporosis with pathological fracture",
"Osteoporosis without pathological fracture",
"Other disorders of bone density and structure",
"Other disorders of bone",
"Postprocedural musculoskeletal disorders, not elsewhere classified",
"Recurrent and persistent haematuria",
"Chronic kidney disease, stage 3",
"Chronic kidney disease, stage 4",
"Other disorders of kidney and ureter, not elsewhere classified",
"Other disorders of urinary system",
"Other disorders of penis",
"Other female pelvic inflammatory diseases",
"Other inflammation of vagina and vulva",
"Other noninflammatory disorders of cervix uteri",
"Other noninflammatory disorders of vagina",
"Other noninflammatory disorders of vulva and perineum",
"Excessive, frequent and irregular menstruation",
"Other abnormal uterine and vaginal bleeding",
"Pain and other conditions associated with female genital organs and menstrual cycle",
"Postprocedural disorders of genitourinary system, not elsewhere classified",
"Pre-eclampsia",
"Medical abortion",
"Maternal care for other conditions predominantly related to pregnancy",
"Maternal care for known or suspected malpresentation of fetus",
"Maternal care for known or suspected abnormality of pelvic organs",
"Maternal care for other known or suspected fetal problems",
"Labour and delivery complicated by fetal stress [distress]",
"Other complications of labour and delivery, not elsewhere classified",
"Other maternal diseases classifiable elsewhere but complicating pregnancy, childbirth and the puerperium",
"Abnormal blood-pressure reading, without diagnosis",
"Pain in throat and chest",
"Other symptoms and signs involving the circulatory and respiratory systems",
"Abdominal and pelvic pain",
"Other symptoms and signs involving the digestive system and abdomen",
"Other symptoms and signs involving the nervous and musculoskeletal systems",
"Tendency to fall, not elsewhere classified",
"Other symptoms and signs involving the urinary system",
"Somnolence, stupor and coma",
"Speech disturbances, not elsewhere classified",
"Shock, not elsewhere classified",
"Other complications of internal prosthetic devices, implants and grafts, not elsewhere classified",
"Foreign body entering into or through eye or natural orifice",
"Nosocomial condition",
"Personal history of endocrine, nutritional and metabolic diseases",
"Personal history of diseases of the musculoskeletal system and connective tissue",
"Personal history of diseases of the genitourinary system",
"Personal history of congenital malformations, deformations and chromosomal abnormalities",
"Personal history of other specified conditions",
"Other complications of internal prosthetic devices, implants and grafts, not elsewhere classified",
"Personal history of allergy, other than to drugs and biological substances",
"Personal history of allergy to unspecified drugs, medicaments and biological substances",
"Personal history of allergy to other drugs, medicaments and biological substances
",
"Personal history of allergy to drugs, medicaments and biological substances",
"Personal history of chemotherapy for neoplastic disease",
"Other noninflammatory disorders of vulva and perineum",
"Resistance to betalactam antibiotics")
)manual_icd10_map <-
readxl::read_xlsx(here::here("data/icd/manual_disease_icd10_mappings.xlsx"))
icd10_descriptions =
phecodes |>
select(icd10_code = ICD10,
icd10_description = ICD_DESCRIPTION
) |>
distinct()
# Expand multiple ICD codes into rows
to_add_expanded <- manual_icd10_map |>
mutate(icd10_code = str_split(icd10_code, ",\\s*")) |>
tidyr::unnest(icd10_code)
icd10_descriptions =
bind_rows(
icd10_descriptions,
to_add_expanded |>
select(icd10_code,
icd10_description = icd10_desc),
other_icd10_desc
)
icd10_descriptions = icd10_descriptions |> distinct()
icd10_descriptions =
icd10_descriptions |>
group_by(icd10_code) |>
summarise(icd10_description =
str_flatten(unique(icd10_description), collapse = "; ", na.rm = T),
.groups = "drop"
)
disease_mapping =
left_join(disease_mapping,
icd10_descriptions,
by = "icd10_code",
relationship = "many-to-one",
na_matches = "never"
)
disease_mapping =
disease_mapping |>
mutate(icd10_code = str_replace_all(
icd10_code,
pattern = "R871",
replacement = "R87"
)
)
disease_mapping =
disease_mapping |>
mutate(icd10_description =
ifelse(icd10_code == "R87",
"Abnormal findings in specimens from female genital organs",
icd10_description)
) # check if any ICD10 codes are missing descriptions
disease_mapping |>
filter(is.na(icd10_description)) |>
head()# A tibble: 6 × 7
`DISEASE/TRAIT` collected_all_diseas…¹ PUBMED_ID phecode icd10_code
<chr> <chr> <int> <dbl> <chr>
1 Ribavirin-induced anemia anemia 20637204 NA D63.165.8
2 Iron deficiency anemia 21483845 NA D63.165.8
3 Source of report of D64 (… anemia 36779085 NA D63.165.8
4 Anemia in mycophenolic ac… anemia 30801552 NA D63.165.8
5 Genital aphthosis in Behc… genital aphthosis 37271218 NA <NA>
6 Deferral due to hypohemog… anemia 38018286 NA D63.165.8
# ℹ abbreviated name: ¹collected_all_disease_terms
# ℹ 2 more variables: icd10_code_origin <chr>, icd10_description <chr>gwas_study_info |>
filter(grepl("ICD10 F05",
`DISEASE/TRAIT`)) |>
select(`DISEASE/TRAIT`, MAPPED_TRAIT, collected_all_disease_terms, PUBMED_ID) DISEASE/TRAIT
<char>
1: ICD10 F05: Delirium due to known physiological condition (Gene-based burden)
2: ICD10 F05.9: Delirium, unspecified (Gene-based burden)
3: ICD10 F05.9: Delirium, unspecified
4: ICD10 F05: Delirium due to known physiological condition
MAPPED_TRAIT collected_all_disease_terms PUBMED_ID
<char> <char> <int>
1: alcohol withdrawal delirium alcohol-related disorders 34662886
2: delirium delirium 34662886
3: delirium delirium 34662886
4: alcohol withdrawal delirium alcohol-related disorders 34662886disease_mapping |>
filter(icd10_code == "F05")# A tibble: 2 × 7
`DISEASE/TRAIT` collected_all_diseas…¹ PUBMED_ID phecode icd10_code
<chr> <chr> <int> <dbl> <chr>
1 ICD10 F05: Delirium due t… alcohol-related disor… 34662886 NA F05
2 ICD10 F05: Delirium due t… alcohol-related disor… 34662886 NA F05
# ℹ abbreviated name: ¹collected_all_disease_terms
# ℹ 2 more variables: icd10_code_origin <chr>, icd10_description <chr># F05 refers to delirium not induced by alcohol and other psychoactive substances
# yet, the mapped trait is alcohol withdrawal delirium
# replace with delirium
disease_mapping =
disease_mapping |>
mutate(collected_all_disease_terms =
ifelse(icd10_code == "F05",
"delirium",
collected_all_disease_terms)
)
gwas_study_info =
gwas_study_info |>
mutate(MAPPED_TRAIT =
ifelse(grepl("ICD10 F05", `DISEASE/TRAIT`),
str_replace_all(collected_all_disease_terms,
pattern = "alcohol-related disorders",
replacement = "delirium"),
collected_all_disease_terms)
)disease_mapping =
disease_mapping |>
arrange(collected_all_disease_terms, icd10_code)
fwrite(disease_mapping,
here::here("output/icd_map/gwas_disease_to_icd10_mapping.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 data.table_1.17.8 stringr_1.5.1
[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 tidyr_1.3.1 callr_3.7.6
[9] later_1.4.2 jquerylib_0.1.4 readxl_1.4.5 yaml_2.3.10
[13] fastmap_1.2.0 here_1.0.1 R6_2.6.1 generics_0.1.4
[17] knitr_1.50 tibble_3.3.0 rprojroot_2.1.0 bslib_0.9.0
[21] pillar_1.11.0 rlang_1.1.6 utf8_1.2.6 cachem_1.1.0
[25] stringi_1.8.7 httpuv_1.6.16 xfun_0.52 getPass_0.2-4
[29] fs_1.6.6 sass_0.4.10 cli_3.6.5 withr_3.0.2
[33] magrittr_2.0.3 ps_1.9.1 digest_0.6.37 processx_3.8.6
[37] rstudioapi_0.17.1 lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.4
[41] glue_1.8.0 cellranger_1.1.0 whisker_0.4.1 purrr_1.1.0
[45] rmarkdown_2.29 tools_4.3.1 pkgconfig_2.0.3 htmltools_0.5.8.1