Region Merge Test
Last updated: 2023-12-20
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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library(ctwas)
library(data.table)
source("/project/xinhe/shengqian/cTWAS_simulation/summarize_basic_plots.R")
Attaching package: 'ggpubr'The following object is masked from 'package:cowplot':
get_legendsource("/project/xinhe/shengqian/cTWAS_simulation/summarize_ctwas_plots.R")
Attaching package: 'plyr'The following object is masked from 'package:ggpubr':
mutateoutputdir1 = "/project2/mstephens/causalTWAS/simulations/simulation_ctwas_rss_20210416/"
outputdir2 = "/project/xinhe/shengqian/cTWAS_simulation/simulation_ctwas_rss_20210416/"
outputdir3 = "/project/xinhe/shengqian/cTWAS_simulation/simulation_ctwas_rss_20210416_mergeoff//"
runtag = "ukb-s80.45-adi"
configtag = 1
configtag1 = 2PIP calibration
PIP plot under different settings.
UKBB individual genotype data. PredictedDB Liver weights. UKBB LD matrix. Gene PVE = 0.05 and SNP PVE = 0.3.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.
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] plyr_1.8.8 ggpubr_0.6.0 plotrix_3.8-4 cowplot_1.1.1
[5] ggplot2_3.4.0 data.table_1.14.6 ctwas_0.1.40 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 lattice_0.20-44 tidyr_1.3.0 getPass_0.2-2
[5] ps_1.7.2 assertthat_0.2.1 rprojroot_2.0.3 digest_0.6.31
[9] foreach_1.5.2 utf8_1.2.2 R6_2.5.1 backports_1.2.1
[13] evaluate_0.19 highr_0.9 httr_1.4.4 pillar_1.8.1
[17] rlang_1.1.1 rstudioapi_0.14 car_3.1-1 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 munsell_0.5.0 broom_1.0.2
[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 gridExtra_2.3 tibble_3.1.8
[37] logging_0.10-108 codetools_0.2-18 fansi_1.0.3 crayon_1.5.2
[41] dplyr_1.0.10 withr_2.5.0 later_1.3.0 grid_4.1.0
[45] jsonlite_1.8.4 gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3
[49] git2r_0.30.1 magrittr_2.0.3 scales_1.2.1 carData_3.0-4
[53] cli_3.6.1 stringi_1.7.8 cachem_1.0.6 farver_2.1.0
[57] ggsignif_0.6.4 fs_1.5.2 promises_1.2.0.1 pgenlibr_0.3.2
[61] bslib_0.4.1 vctrs_0.6.3 generics_0.1.3 iterators_1.0.14
[65] tools_4.1.0 glue_1.6.2 purrr_1.0.2 abind_1.4-5
[69] processx_3.8.0 fastmap_1.1.0 yaml_2.3.6 colorspace_2.0-3
[73] rstatix_0.7.2 knitr_1.41 sass_0.4.4