Last updated: 2024-12-10

Checks: 6 1

Knit directory: multigroup_ctwas_analysis/

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Rmd 7c48b48 sq-96 2024-12-10 update
html 7c48b48 sq-96 2024-12-10 update
Rmd e30c27a sq-96 2024-12-10 update
html e30c27a sq-96 2024-12-10 update
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Rmd 2f0187d sq-96 2024-12-06 update
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Rmd e75361e sq-96 2024-12-03 update
html e75361e sq-96 2024-12-03 update
Rmd 71c46d3 sq-96 2024-12-03 update
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Method

  1. Run all tissues jointly (very fast if weights have been harmonized).
  2. Rank tissues by %h2g and select reasonable top ones.

Summary

  1. For IBD, colon transverse and whole blood have much higher %h2g than other tissues.
  2. For LDL, liver has much higher %h2g than other tissues.
  3. For SBP, the top five ones all make sense, which are artery aorta, brain cortex, artery tibial, cell cultured fibroblasts and adrenal gland.
  4. For WBC, whole blood has much higher %h2g than other tissues.
  5. For SCZ, the top ones are basal ganglia, cerebellum, hippocampus, hemisphere, cortex …

IBD results (Inflammatory bowel disease)

WBC results (White blood cell count)

RA results (Rheumatoid arthritis)

SBP results (Systolic blood pressure)

DBP results (Diastolic blood pressure)

HTN results (Hypertension)

SCZ results (Schizophrenia)

BIP results (Bipolar disorder)

MDD results (Major depressive disorder)

LDL results (low-density lipoprotein)

TG results (Triglycerides)

BMI results (Body mass index)

T2D results (Type 2 diabetes)


sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.13       compiler_4.2.0    pillar_1.9.0      bslib_0.8.0      
 [5] later_1.3.2       git2r_0.30.1      jquerylib_0.1.4   tools_4.2.0      
 [9] getPass_0.2-2     digest_0.6.37     jsonlite_1.8.9    evaluate_1.0.0   
[13] lifecycle_1.0.4   tibble_3.2.1      pkgconfig_2.0.3   rlang_1.1.4      
[17] cli_3.6.3         rstudioapi_0.14   crosstalk_1.2.1   yaml_2.3.10      
[21] xfun_0.47         fastmap_1.2.0     httr_1.4.7        stringr_1.5.1    
[25] knitr_1.48        htmlwidgets_1.6.4 sass_0.4.9        fs_1.6.4         
[29] vctrs_0.6.5       DT_0.22           rprojroot_2.0.3   glue_1.7.0       
[33] R6_2.5.1          processx_3.7.0    fansi_1.0.6       rmarkdown_2.28   
[37] callr_3.7.2       magrittr_2.0.3    whisker_0.4       ps_1.7.1         
[41] promises_1.3.0    htmltools_0.5.8.1 httpuv_1.6.5      utf8_1.2.4       
[45] stringi_1.8.4     cachem_1.1.0