LDL - Liver and Adipose - E and S
2023-12-30
Last updated: 2024-01-05
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | a430848 | sq-96 | 2024-01-04 | update |
| html | a430848 | sq-96 | 2024-01-04 | update |
| Rmd | 690e29e | sq-96 | 2024-01-03 | update |
Load ctwas results
outputdir <- "/project/xinhe/shengqian/cTWAS_analysis/data/test_context/"
outname <- "test_context_ctwas"
gwas_n <- 343621
thin <- 0.1
ctwas_parameters <- ctwas:::ctwas_summarize_parameters(outputdir = outputdir,
outname = outname,
gwas_n = 343621,
thin = 0.1,
plot_estimates = T)
Top genes by combined PIP
Context/Type Contributions
plot_stacked_histogram(plot_df,"genename","combined_pip",colnames(plot_df)[3:6])Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation ideoms with `aes()`
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.
| Version | Author | Date |
|---|---|---|
| a430848 | sq-96 | 2024-01-04 |
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] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] tidyr_1.3.0 dplyr_1.0.10 DT_0.26 RSQLite_2.2.19
[5] data.table_1.14.6 ctwas_0.1.40 cowplot_1.1.1 ggplot2_3.4.0
[9] 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 evaluate_0.19 httr_1.4.4
[13] highr_0.9 pillar_1.8.1 rlang_1.1.1 rstudioapi_0.14
[17] whisker_0.4.1 callr_3.7.3 jquerylib_0.1.4 blob_1.2.3
[21] Matrix_1.3-3 rmarkdown_2.19 labeling_0.4.2 stringr_1.5.0
[25] htmlwidgets_1.6.0 bit_4.0.5 munsell_0.5.0 compiler_4.1.0
[29] httpuv_1.6.7 xfun_0.35 pkgconfig_2.0.3 htmltools_0.5.4
[33] tidyselect_1.2.0 tibble_3.1.8 logging_0.10-108 codetools_0.2-18
[37] fansi_1.0.3 crayon_1.5.2 withr_2.5.0 later_1.3.0
[41] grid_4.1.0 jsonlite_1.8.4 gtable_0.3.1 lifecycle_1.0.3
[45] DBI_1.1.3 git2r_0.30.1 magrittr_2.0.3 scales_1.2.1
[49] cli_3.6.1 stringi_1.7.8 cachem_1.0.6 farver_2.1.0
[53] fs_1.5.2 promises_1.2.0.1 pgenlibr_0.3.2 bslib_0.4.1
[57] ellipsis_0.3.2 vctrs_0.6.3 generics_0.1.3 iterators_1.0.14
[61] bit64_4.0.5 glue_1.6.2 purrr_1.0.2 crosstalk_1.2.0
[65] processx_3.8.0 fastmap_1.1.0 yaml_2.3.6 colorspace_2.0-3
[69] memoise_2.0.1 knitr_1.41 sass_0.4.4