Last updated: 2022-02-17
Checks: 6 1
Knit directory: codemapper/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5c2a3e3 | Chuin Ying Ung | 2022-02-17 | update _targets.R (housekeeping) and phecode.Rmd |
| html | 5c2a3e3 | Chuin Ying Ung | 2022-02-17 | update _targets.R (housekeeping) and phecode.Rmd |
| Rmd | 8d14804 | Chuin Ying Ung | 2022-02-17 | add phecode.Rmd |
Aim: to explore the phecode lookup and mapping files.
DOWNLOAD PHECODE MAPPING FILES TO DATA DIRECTORY,THEN LOAD INTO R
How many ICD-10 codes are included in the UK Biobank lookup table? (head shown below)
# A tibble: 17,934 × 12
ICD10_CODE ALT_CODE USAGE USAGE_UK DESCRIPTION MODIFIER_4 MODIFIER_5
<chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 A00 A00 DEFAULT 3 Cholera <NA> <NA>
2 A00.0 A000 DEFAULT 3 Cholera due to Vi… <NA> <NA>
3 A00.1 A001 DEFAULT 3 Cholera due to Vi… <NA> <NA>
4 A00.9 A009 DEFAULT 3 Cholera, unspecif… <NA> <NA>
5 A01 A01 DEFAULT 3 Typhoid and parat… <NA> <NA>
6 A01.0 A010 DEFAULT 3 Typhoid fever <NA> <NA>
7 A01.1 A011 DEFAULT 3 Paratyphoid fever… <NA> <NA>
8 A01.2 A012 DEFAULT 3 Paratyphoid fever… <NA> <NA>
9 A01.3 A013 DEFAULT 3 Paratyphoid fever… <NA> <NA>
10 A01.4 A014 DEFAULT 3 Paratyphoid fever… <NA> <NA>
# … with 17,924 more rows, and 5 more variables: QUALIFIERS <chr>,
# GENDER_MASK <chr>, MIN_AGE <chr>, MAX_AGE <chr>, TREE_DESCRIPTION <chr>
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats graphics grDevices datasets utils methods
[8] base
other attached packages:
[1] PheWAS_0.99.5-5 codemapper_0.0.0.9000 ukbwranglr_0.0.0.9000
[4] targets_0.8.0 crosstalk_1.1.1 readxl_1.3.1
[7] reactable_0.2.3 forcats_0.5.1 stringr_1.4.0
[10] dplyr_1.0.7 purrr_0.3.4 readr_2.0.2
[13] tidyr_1.1.4 tibble_3.1.4 ggplot2_3.3.5
[16] tidyverse_1.3.1 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] minqa_1.2.4 colorspace_2.0-2 ellipsis_0.3.2
[4] rprojroot_2.0.2 fs_1.5.0 rstudioapi_0.13
[7] mice_3.14.0 ggrepel_0.9.1 DT_0.20
[10] fansi_0.5.0 lubridate_1.7.10 mathjaxr_1.4-0
[13] xml2_1.3.2 codetools_0.2-18 splines_4.1.0
[16] knitr_1.34 jsonlite_1.7.2 nloptr_2.0.0
[19] logistf_1.24.1 broom_0.7.9 dbplyr_2.1.1
[22] shiny_1.7.0 compiler_4.1.0 httr_1.4.2
[25] backports_1.2.1 assertthat_0.2.1 Matrix_1.3-3
[28] fastmap_1.1.0 cli_3.0.1 later_1.3.0
[31] htmltools_0.5.2 tools_4.1.0 igraph_1.2.6
[34] gtable_0.3.0 glue_1.4.2 Rcpp_1.0.7
[37] cellranger_1.1.0 jquerylib_0.1.4 vctrs_0.3.8
[40] nlme_3.1-152 lmtest_0.9-39 xfun_0.24
[43] ps_1.6.0 lme4_1.1-28 rvest_1.0.1
[46] mime_0.12 CompQuadForm_1.4.3 lifecycle_1.0.1
[49] renv_0.13.2 formula.tools_1.7.1 MASS_7.3-54
[52] zoo_1.8-9 scales_1.1.1 hms_1.1.1
[55] promises_1.2.0.1 meta_5.2-0 metafor_3.0-2
[58] yaml_2.2.1 sass_0.4.0 stringi_1.7.4
[61] highr_0.9 boot_1.3-28 operator.tools_1.6.3
[64] rlang_0.4.11 pkgconfig_2.0.3 evaluate_0.14
[67] lattice_0.20-44 htmlwidgets_1.5.4 processx_3.5.2
[70] tidyselect_1.1.1 magrittr_2.0.1 R6_2.5.1
[73] generics_0.1.0 DBI_1.1.1 pillar_1.6.3
[76] haven_2.4.3 whisker_0.4 withr_2.4.2
[79] mgcv_1.8-35 survival_3.2-13 modelr_0.1.8
[82] crayon_1.4.1 utf8_1.2.2 tzdb_0.1.2
[85] rmarkdown_2.11 grid_4.1.0 data.table_1.14.2
[88] callr_3.7.0 git2r_0.28.0 reprex_2.0.1
[91] digest_0.6.28 xtable_1.8-4 httpuv_1.6.3
[94] munsell_0.5.0 bslib_0.3.0