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UKBB phenotyping example

ukbb_phenotyping.Rmd
library(heRmes)
#> Warning: no DISPLAY variable so Tk is not available

Example phenotyping of UKBB data

Phenotyping of the UK biobank hospital admissions data.

pheno_ukbb <- phenotype(file_path, 
                        id_col    = "eid", 
                        code_cols = list("ICD10 codes" = "diag_icd10", "ICD9 codes" = "diag_icd9"),
                        include   = list(HF  = "PH1645", CM = "PH1646"), 
                        exclude   = list(congHD = "PH1637", MI = "PH1636", HCM = "PH1640"), 
                        gsub      = list("\\.", "", c("x")),
                        name      = "Heart Failure")

plot(eulerr::euler(pheno_ukbb[, mget(names(pheno_ukbb)[!names(pheno_ukbb) %in% c("eid", "none")])], shape = "circle"),
          quantities = TRUE,
          labels     = FALSE,
          main       = list(label = "UKBB Heart failure phenotyping", fontsize = 8, font = 2),
          legend     = list(fontsize = 8))

Plot the ICD-10 HERMES phenotypes

Plot the overlap of the HERMES phenotypes with all other heart failure phenotypes in the UKHDR Phenotype library.

plot_code_overlap(pheno_ids = hermes_phenos, types = c("ICD10 codes"))

Co-occurrence of UKBB ICD-10 codes

Co-occurrence matrix of heart failure (PH1645) and cardiomyopathy (PH1646) codes.