OxHb

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Last updated: 2023-10-14

Checks: 5 2

Knit directory: cTWAS_analysis/

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Untracked files:
    Untracked:  LDL_LDLR_locus1.pdf
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/OxHB.Rmd) and HTML (docs/OxHB.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
Rmd	d04dec9	sq-96	2023-10-14	update
html	d04dec9	sq-96	2023-10-14	update
html	f442f0e	sq-96	2023-10-14	update
Rmd	6a15ad1	sq-96	2023-10-14	update
html	6a15ad1	sq-96	2023-10-14	update
Rmd	e0d796f	sq-96	2023-10-13	update

---

Artery Coronary

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003789661 0.0048196252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6727008 0.5860888 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
12.71783 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.71103798 0.01352419 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7245622

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98133467 0.01866533 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-3-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

#print top genes
head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
164440     9 ENSG00000136868.10 113209149 gene           9          58        0
263152    20 ENSG00000089177.18  16581461 gene          20          12        0
272677    22 ENSG00000184381.18  38145259 gene          22          15        0
261678    20  ENSG00000275491.1   3807832 gene          20           3        0
90495      5 ENSG00000132356.11  40798520 gene           5          27        0
117969     6 ENSG00000178425.13 116099964 gene           6          77        0
        susie_pip      mu2  genename         z
164440 0.11803156 9.216227   SLC31A1 -3.933203
263152 0.09730827 8.050336    KIF16B -3.085439
272677 0.08515657 7.548930    PLA2G6  3.053686
261678 0.08398874 7.466874 LINC01730 -2.945771
90495  0.08384722 7.723628    PRKAA1 -3.439407
117969 0.08334959 7.383582    NT5DC1  3.118395

Artery Tibial

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003778214 0.0040115252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6684344 0.5565171 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.61752 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.70439414 0.01309908 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7174932

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98174327 0.01825673 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-7-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
114696     6 ENSG00000005700.14  82247064 gene           6          56        0
272419    22 ENSG00000159496.14  23679302 gene          22           6        0
179945    10 ENSG00000151923.17 119601669 gene          10          74        0
151888     8  ENSG00000164841.4 108787887 gene           8          74        0
241123    16 ENSG00000040199.18  71804965 gene          16          38        0
243700    17 ENSG00000174292.12   7380407 gene          17           6        0
        susie_pip      mu2 genename         z
114696 0.11468988 9.126035     IBTK -3.787795
272419 0.08483873 7.971765     RGL4  3.286735
179945 0.08104538 7.839875    TIAL1  3.480318
151888 0.07962949 7.989882   TMEM74 -3.623924
241123 0.07790796 7.513540   PHLPP2 -3.126064
243700 0.07591772 7.535001     TNK1  3.186510

Heart Atrial Appendage

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003778214 0.0040115252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6684344 0.5565171 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.61752 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.70439414 0.01309908 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7174932

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98174327 0.01825673 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-11-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
114696     6 ENSG00000005700.14  82247064 gene           6          56        0
272419    22 ENSG00000159496.14  23679302 gene          22           6        0
179945    10 ENSG00000151923.17 119601669 gene          10          74        0
151888     8  ENSG00000164841.4 108787887 gene           8          74        0
241123    16 ENSG00000040199.18  71804965 gene          16          38        0
243700    17 ENSG00000174292.12   7380407 gene          17           6        0
        susie_pip      mu2 genename         z
114696 0.11468988 9.126035     IBTK -3.787795
272419 0.08483873 7.971765     RGL4  3.286735
179945 0.08104538 7.839875    TIAL1  3.480318
151888 0.07962949 7.989882   TMEM74 -3.623924
241123 0.07790796 7.513540   PHLPP2 -3.126064
243700 0.07591772 7.535001     TNK1  3.186510

Heart Left Ventricle

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003778214 0.0040115252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6684344 0.5565171 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.61752 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.70439414 0.01309908 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7174932

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98174327 0.01825673 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-15-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
114696     6 ENSG00000005700.14  82247064 gene           6          56        0
272419    22 ENSG00000159496.14  23679302 gene          22           6        0
179945    10 ENSG00000151923.17 119601669 gene          10          74        0
151888     8  ENSG00000164841.4 108787887 gene           8          74        0
241123    16 ENSG00000040199.18  71804965 gene          16          38        0
243700    17 ENSG00000174292.12   7380407 gene          17           6        0
        susie_pip      mu2 genename         z
114696 0.11468988 9.126035     IBTK -3.787795
272419 0.08483873 7.971765     RGL4  3.286735
179945 0.08104538 7.839875    TIAL1  3.480318
151888 0.07962949 7.989882   TMEM74 -3.623924
241123 0.07790796 7.513540   PHLPP2 -3.126064
243700 0.07591772 7.535001     TNK1  3.186510

Kidney Cortex

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003778214 0.0040115252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6684344 0.5565171 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.61752 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.70439414 0.01309908 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7174932

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98174327 0.01825673 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-19-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
114696     6 ENSG00000005700.14  82247064 gene           6          56        0
272419    22 ENSG00000159496.14  23679302 gene          22           6        0
179945    10 ENSG00000151923.17 119601669 gene          10          74        0
151888     8  ENSG00000164841.4 108787887 gene           8          74        0
241123    16 ENSG00000040199.18  71804965 gene          16          38        0
243700    17 ENSG00000174292.12   7380407 gene          17           6        0
        susie_pip      mu2 genename         z
114696 0.11468988 9.126035     IBTK -3.787795
272419 0.08483873 7.971765     RGL4  3.286735
179945 0.08104538 7.839875    TIAL1  3.480318
151888 0.07962949 7.989882   TMEM74 -3.623924
241123 0.07790796 7.513540   PHLPP2 -3.126064
243700 0.07591772 7.535001     TNK1  3.186510

Liver

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003778214 0.0040115252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6684344 0.5565171 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.61752 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.70439414 0.01309908 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7174932

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98174327 0.01825673 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-23-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
114696     6 ENSG00000005700.14  82247064 gene           6          56        0
272419    22 ENSG00000159496.14  23679302 gene          22           6        0
179945    10 ENSG00000151923.17 119601669 gene          10          74        0
151888     8  ENSG00000164841.4 108787887 gene           8          74        0
241123    16 ENSG00000040199.18  71804965 gene          16          38        0
243700    17 ENSG00000174292.12   7380407 gene          17           6        0
        susie_pip      mu2 genename         z
114696 0.11468988 9.126035     IBTK -3.787795
272419 0.08483873 7.971765     RGL4  3.286735
179945 0.08104538 7.839875    TIAL1  3.480318
151888 0.07962949 7.989882   TMEM74 -3.623924
241123 0.07790796 7.513540   PHLPP2 -3.126064
243700 0.07591772 7.535001     TNK1  3.186510

Lung

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003778214 0.0040115252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6684344 0.5565171 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.61752 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.70439414 0.01309908 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7174932

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98174327 0.01825673 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-27-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
114696     6 ENSG00000005700.14  82247064 gene           6          56        0
272419    22 ENSG00000159496.14  23679302 gene          22           6        0
179945    10 ENSG00000151923.17 119601669 gene          10          74        0
151888     8  ENSG00000164841.4 108787887 gene           8          74        0
241123    16 ENSG00000040199.18  71804965 gene          16          38        0
243700    17 ENSG00000174292.12   7380407 gene          17           6        0
        susie_pip      mu2 genename         z
114696 0.11468988 9.126035     IBTK -3.787795
272419 0.08483873 7.971765     RGL4  3.286735
179945 0.08104538 7.839875    TIAL1  3.480318
151888 0.07962949 7.989882   TMEM74 -3.623924
241123 0.07790796 7.513540   PHLPP2 -3.126064
243700 0.07591772 7.535001     TNK1  3.186510

Pancreas

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003778214 0.0040115252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6684344 0.5565171 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.61752 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.70439414 0.01309908 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7174932

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98174327 0.01825673 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-31-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
114696     6 ENSG00000005700.14  82247064 gene           6          56        0
272419    22 ENSG00000159496.14  23679302 gene          22           6        0
179945    10 ENSG00000151923.17 119601669 gene          10          74        0
151888     8  ENSG00000164841.4 108787887 gene           8          74        0
241123    16 ENSG00000040199.18  71804965 gene          16          38        0
243700    17 ENSG00000174292.12   7380407 gene          17           6        0
        susie_pip      mu2 genename         z
114696 0.11468988 9.126035     IBTK -3.787795
272419 0.08483873 7.971765     RGL4  3.286735
179945 0.08104538 7.839875    TIAL1  3.480318
151888 0.07962949 7.989882   TMEM74 -3.623924
241123 0.07790796 7.513540   PHLPP2 -3.126064
243700 0.07591772 7.535001     TNK1  3.186510

Whole_Blood

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003778214 0.0040115252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6684344 0.5565171 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.61752 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.70439414 0.01309908 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7174932

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98174327 0.01825673 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-35-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
114696     6 ENSG00000005700.14  82247064 gene           6          56        0
272419    22 ENSG00000159496.14  23679302 gene          22           6        0
179945    10 ENSG00000151923.17 119601669 gene          10          74        0
151888     8  ENSG00000164841.4 108787887 gene           8          74        0
241123    16 ENSG00000040199.18  71804965 gene          16          38        0
243700    17 ENSG00000174292.12   7380407 gene          17           6        0
        susie_pip      mu2 genename         z
114696 0.11468988 9.126035     IBTK -3.787795
272419 0.08483873 7.971765     RGL4  3.286735
179945 0.08104538 7.839875    TIAL1  3.480318
151888 0.07962949 7.989882   TMEM74 -3.623924
241123 0.07790796 7.513540   PHLPP2 -3.126064
243700 0.07591772 7.535001     TNK1  3.186510

Session information

sessionInfo()

R version 4.1.0 (2021-05-18)
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] cowplot_1.1.1   ggplot2_3.4.0   ctwas_0.1.40    workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9        lattice_0.20-44   getPass_0.2-2     ps_1.7.2         
 [5] assertthat_0.2.1  rprojroot_2.0.3   digest_0.6.31     foreach_1.5.2    
 [9] utf8_1.2.2        R6_2.5.1          RSQLite_2.2.19    evaluate_0.19    
[13] httr_1.4.4        highr_0.9         pillar_1.8.1      rlang_1.1.1      
[17] rstudioapi_0.14   data.table_1.14.6 blob_1.2.3        whisker_0.4.1    
[21] callr_3.7.3       jquerylib_0.1.4   Matrix_1.3-3      rmarkdown_2.19   
[25] labeling_0.4.2    stringr_1.5.0     bit_4.0.5         munsell_0.5.0    
[29] compiler_4.1.0    httpuv_1.6.7      xfun_0.35         pkgconfig_2.0.3  
[33] htmltools_0.5.4   tidyselect_1.2.0  tibble_3.1.8      logging_0.10-108 
[37] codetools_0.2-18  fansi_1.0.3       dplyr_1.0.10      withr_2.5.0      
[41] later_1.3.0       grid_4.1.0        jsonlite_1.8.4    gtable_0.3.1     
[45] lifecycle_1.0.3   DBI_1.1.3         git2r_0.30.1      magrittr_2.0.3   
[49] scales_1.2.1      cli_3.6.1         stringi_1.7.8     cachem_1.0.6     
[53] farver_2.1.0      fs_1.5.2          promises_1.2.0.1  pgenlibr_0.3.2   
[57] bslib_0.4.1       vctrs_0.6.3       generics_0.1.3    iterators_1.0.14 
[61] tools_4.1.0       bit64_4.0.5       glue_1.6.2        processx_3.8.0   
[65] fastmap_1.1.0     yaml_2.3.6        colorspace_2.0-3  memoise_2.0.1    
[69] knitr_1.41        sass_0.4.4