Reformatting UKB ‘all_lkps_maps.xlsx’
Alasdair Warwick
22 February, 2022
Last updated: 2022-02-22
Checks: 5 2
Knit directory: codemapper/
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/phecodes.Rmd) and HTML (public/phecodes.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | d777258 | Chuin Ying Ung | 2022-02-22 | merge with dev_cy branch |
| html | 1df97df | rmgpanw | 2022-02-17 | incorporate icd9 and icd10 to phecode maps |
| html | 81047b4 | rmgpanw | 2022-02-17 | setup for gitlab CI with pkgdown site and test coverage; start adding read3 to snomed mapping |
| Rmd | 1535c93 | Chuin Ying Ung | 2022-02-17 | updated notes |
| html | 1535c93 | Chuin Ying Ung | 2022-02-17 | updated notes |
| 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 |
Overview
Aim: to explore the phecode lookup and mapping files.
Background - phecodes
- LINKS TO KEY PUBLICATIONS AND WEBPAGES
- WHAT CODING SYSTEM IS PHECODES BASED ON, AND WHICH CLINICAL CODES CAN BE MAPPED TO THIS?
PheWAS R package
- READ HELP PAGE FROM RUNNING BELOW
- TO START, PERHAPS TRY RUNNING THE EXAMPLE (AT BOTTOM OF HELP PAGE) - COPY AND PASTE INTO THIS NOTEBOOK SO WE CAN SEE THE OUTPUT AT EACH STEP
Generate some example data
#Create the phecode table- translates the codes, adds exclusions, and reshapes to a wide format. #Sum up the counts in the data where applicable.
#Combine the data
#Run the PheWAS
#Plot the results 
| Version | Author | Date |
|---|---|---|
| 1535c93 | Chuin Ying Ung | 2022-02-17 |
#Add PheWAS descriptions
#List the top 10 results
phenotype snp covariates beta SE OR
549 335 rsEXAMPLE sex 0.3967548 0.06684421 1.4869913
431 288.2 rsEXAMPLE sex 1.3847304 0.38379930 3.9937489
507 315.1 rsEXAMPLE sex 1.4280228 0.41430554 4.1704451
1475 716.8 rsEXAMPLE sex 1.3794156 0.40731579 3.9725795
1686 798.1 rsEXAMPLE sex 1.0432921 0.30938935 2.8385463
743 401.2 rsEXAMPLE sex 0.8005488 0.24653912 2.2267626
1002 525.1 rsEXAMPLE sex 0.9682267 0.29931207 2.6332707
680 375.1 rsEXAMPLE sex -1.2438354 0.38503286 0.2882764
838 440.2 rsEXAMPLE sex 0.6394982 0.20822694 1.8955294
744 401.21 rsEXAMPLE sex 1.2694273 0.41871628 3.5588138
p type n_total n_cases n_controls HWE_p allele_freq
549 2.929243e-09 logistic 4404 1873 2531 1 0.5128292
431 3.086207e-04 logistic 4731 26 4705 1 0.5110970
507 5.672965e-04 logistic 4762 22 4740 1 0.5115498
1475 7.076450e-04 logistic 4243 23 4220 1 0.5103700
1686 7.459717e-04 logistic 4973 42 4931 1 0.5115624
743 1.165681e-03 logistic 4924 70 4854 1 0.5111698
1002 1.217109e-03 logistic 4284 46 4238 1 0.5109711
680 1.235888e-03 logistic 4501 27 4474 1 0.5118862
838 2.132291e-03 logistic 4108 102 4006 1 0.5139971
744 2.431709e-03 logistic 4876 22 4854 1 0.5105619
n_no_snp formula expanded_formula
549 0 `335` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
431 0 `288.2` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
507 0 `315.1` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
1475 0 `716.8` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
1686 0 `798.1` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
743 0 `401.2` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
1002 0 `525.1` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
680 0 `375.1` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
838 0 `440.2` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
744 0 `401.21` ~ `rsEXAMPLE` + `sex` (Intercept) + rsEXAMPLE + sexM
note description group
549 Multiple sclerosis neurological
431 Elevated white blood cell count hematopoietic
507 Learning disorder mental disorders
1475 Palindromic rheumatism musculoskeletal
1686 Chronic fatigue syndrome symptoms
743 Hypertensive heart and/or renal disease circulatory system
1002 Loss of teeth or edentulism digestive
680 Dry eyes sense organs
838 Atherosclerosis of the extremities circulatory system
744 Hypertensive heart disease circulatory system#Create a nice interactive table (eg, in RStudio)
Mapping files
DOWNLOAD PHECODE MAPPING FILES TO DATA DIRECTORY,THEN LOAD INTO R
Downloaded files from ukbb pan ancestry https://github.com/atgu/ukbb_pan_ancestry
How many ICD codes are included in the UK Biobank lookup table? (head shown below)
| Version | Author | Date |
|---|---|---|
| 1535c93 | Chuin Ying Ung | 2022-02-17 |
| Version | Author | Date |
|---|---|---|
| 1535c93 | Chuin Ying Ung | 2022-02-17 |
Which ICD-10 codes are not shared by phecode_map and all_lkps_maps
How many ICD-10 codes map to >1 phecode? (I think this is mentioned on the phecode website, and in Spiros’ github repo readme)
[1] 7017[1] 1004- How many ICD-9 codes map to >1 phecode?
[1] 6917[1] 2772
R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.2
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/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 ggVennDiagram_1.2.0 codemapper_0.0.0.9000
[4] ukbwranglr_0.0.0.9000 targets_0.8.0 crosstalk_1.1.1
[7] readxl_1.3.1 reactable_0.2.3 forcats_0.5.1
[10] stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[13] readr_2.0.2 tidyr_1.1.4 tibble_3.1.4
[16] ggplot2_3.3.5 tidyverse_1.3.1 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] minqa_1.2.4 colorspace_2.0-2 class_7.3-20
[4] ellipsis_0.3.2 rprojroot_2.0.2 fs_1.5.0
[7] proxy_0.4-26 rstudioapi_0.13 mice_3.14.0
[10] farver_2.1.0 bit64_4.0.5 ggrepel_0.9.1
[13] DT_0.20 fansi_0.5.0 lubridate_1.7.10
[16] mathjaxr_1.4-0 xml2_1.3.2 codetools_0.2-18
[19] splines_4.1.2 knitr_1.34 jsonlite_1.7.2
[22] nloptr_2.0.0 logistf_1.24.1 broom_0.7.9
[25] dbplyr_2.1.1 shiny_1.7.0 compiler_4.1.2
[28] httr_1.4.2 backports_1.2.1 assertthat_0.2.1
[31] Matrix_1.3-3 fastmap_1.1.0 cli_3.0.1
[34] later_1.3.0 htmltools_0.5.2 tools_4.1.2
[37] igraph_1.2.6 gtable_0.3.0 glue_1.4.2
[40] Rcpp_1.0.7 cellranger_1.1.0 jquerylib_0.1.4
[43] vctrs_0.3.8 nlme_3.1-152 lmtest_0.9-39
[46] xfun_0.24 ps_1.6.0 lme4_1.1-28
[49] rvest_1.0.1 mime_0.12 CompQuadForm_1.4.3
[52] lifecycle_1.0.1 renv_0.13.2 formula.tools_1.7.1
[55] zoo_1.8-9 MASS_7.3-54 scales_1.1.1
[58] vroom_1.5.5 hms_1.1.1 promises_1.2.0.1
[61] meta_5.2-0 metafor_3.0-2 yaml_2.2.1
[64] sass_0.4.0 stringi_1.7.4 highr_0.9
[67] e1071_1.7-9 boot_1.3-28 operator.tools_1.6.3
[70] rlang_0.4.11 pkgconfig_2.0.3 evaluate_0.14
[73] lattice_0.20-44 sf_1.0-6 labeling_0.4.2
[76] htmlwidgets_1.5.4 bit_4.0.4 processx_3.5.2
[79] tidyselect_1.1.1 magrittr_2.0.1 R6_2.5.1
[82] generics_0.1.0 DBI_1.1.1 pillar_1.6.3
[85] haven_2.4.3 whisker_0.4 withr_2.4.2
[88] mgcv_1.8-35 units_0.8-0 survival_3.2-13
[91] modelr_0.1.8 crayon_1.4.1 KernSmooth_2.23-20
[94] utf8_1.2.2 RVenn_1.1.0 tzdb_0.1.2
[97] rmarkdown_2.11 grid_4.1.2 data.table_1.14.2
[100] reactR_0.4.4 callr_3.7.0 git2r_0.28.0
[103] classInt_0.4-3 reprex_2.0.1 digest_0.6.28
[106] xtable_1.8-4 httpuv_1.6.3 munsell_0.5.0
[109] bslib_0.3.0