simulation_summary
2024-10-02
Last updated: 2025-02-07
Checks: 7 0
Knit directory: multigroup_ctwas_analysis/
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Parameter estimation on all regions (min_gene=0, min_p_single_effect=0, min_var=1)
Parameter estimation on selected regions (min_gene=1, min_p_single_effect=0.8, min_var=2)
PIP calibration (cs index filter)
Enrichment=1 (without cs index filter)
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.Warning: Removed 6 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 6 rows containing missing values or values outside the scale range
(`geom_point()`).
Enrichment=1 (with cs index filter)
Warning: Removed 6 rows containing missing values or values outside the scale range
(`geom_point()`).
Removed 6 rows containing missing values or values outside the scale range
(`geom_point()`).
Enrichment=10 (without cs index filter)
Enrichment=10 (with cs index filter)
Enrichment=80 (without cs index filter)
Enrichment=80 (with cs index filter)
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] plyr_1.8.7 plotrix_3.8-2 cowplot_1.1.3 ggpubr_0.6.0
[5] ggbreak_0.1.2 data.table_1.16.0 ggplot2_3.5.1 dplyr_1.1.4
[9] tidyr_1.3.1 ctwas_0.5.2.9000 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] backports_1.4.1 BiocFileCache_2.6.1
[3] lazyeval_0.2.2 BiocParallel_1.32.6
[5] GenomeInfoDb_1.34.9 LDlinkR_1.4.0
[7] digest_0.6.37 yulab.utils_0.1.7
[9] ensembldb_2.22.0 htmltools_0.5.8.1
[11] fansi_1.0.6 magrittr_2.0.3
[13] memoise_2.0.1 tzdb_0.4.0
[15] Biostrings_2.66.0 readr_2.1.5
[17] matrixStats_1.4.1 locuszoomr_0.3.5
[19] prettyunits_1.2.0 colorspace_2.1-1
[21] blob_1.2.4 rappdirs_0.3.3
[23] ggrepel_0.9.6 xfun_0.47
[25] callr_3.7.2 crayon_1.5.3
[27] RCurl_1.98-1.16 jsonlite_1.8.9
[29] zoo_1.8-12 glue_1.7.0
[31] gtable_0.3.5 zlibbioc_1.44.0
[33] XVector_0.38.0 DelayedArray_0.24.0
[35] car_3.1-1 BiocGenerics_0.44.0
[37] abind_1.4-5 scales_1.3.0
[39] DBI_1.2.3 rstatix_0.7.2
[41] Rcpp_1.0.13 viridisLite_0.4.2
[43] progress_1.2.3 gridGraphics_0.5-1
[45] bit_4.5.0 stats4_4.2.0
[47] htmlwidgets_1.6.4 httr_1.4.7
[49] pkgconfig_2.0.3 XML_3.99-0.14
[51] farver_2.1.2 sass_0.4.9
[53] dbplyr_2.5.0 utf8_1.2.4
[55] labeling_0.4.3 ggplotify_0.1.2
[57] tidyselect_1.2.1 rlang_1.1.4
[59] later_1.3.2 AnnotationDbi_1.60.2
[61] munsell_0.5.1 pgenlibr_0.3.7
[63] tools_4.2.0 cachem_1.1.0
[65] cli_3.6.3 generics_0.1.3
[67] RSQLite_2.3.7 broom_1.0.5
[69] evaluate_1.0.0 stringr_1.5.1
[71] fastmap_1.2.0 yaml_2.3.10
[73] processx_3.7.0 knitr_1.48
[75] bit64_4.5.2 fs_1.6.4
[77] purrr_1.0.2 KEGGREST_1.38.0
[79] AnnotationFilter_1.22.0 whisker_0.4
[81] aplot_0.2.3 xml2_1.3.3
[83] biomaRt_2.54.1 compiler_4.2.0
[85] rstudioapi_0.14 plotly_4.10.4
[87] filelock_1.0.3 curl_5.2.3
[89] png_0.1-7 ggsignif_0.6.3
[91] tibble_3.2.1 bslib_0.8.0
[93] stringi_1.8.4 highr_0.11
[95] ps_1.7.1 GenomicFeatures_1.50.4
[97] lattice_0.20-45 ProtGenerics_1.30.0
[99] Matrix_1.5-3 vctrs_0.6.5
[101] pillar_1.9.0 lifecycle_1.0.4
[103] jquerylib_0.1.4 bitops_1.0-8
[105] irlba_2.3.5.1 httpuv_1.6.5
[107] patchwork_1.3.0 rtracklayer_1.58.0
[109] GenomicRanges_1.50.2 R6_2.5.1
[111] BiocIO_1.8.0 promises_1.3.0
[113] gridExtra_2.3 IRanges_2.32.0
[115] codetools_0.2-18 SummarizedExperiment_1.28.0
[117] rprojroot_2.0.3 rjson_0.2.23
[119] withr_3.0.1 GenomicAlignments_1.34.1
[121] Rsamtools_2.14.0 S4Vectors_0.36.2
[123] GenomeInfoDbData_1.2.9 parallel_4.2.0
[125] hms_1.1.3 grid_4.2.0
[127] ggfun_0.1.6 gggrid_0.2-0
[129] rmarkdown_2.28 MatrixGenerics_1.10.0
[131] carData_3.0-5 logging_0.10-108
[133] git2r_0.30.1 mixsqp_0.3-54
[135] getPass_0.2-2 Biobase_2.58.0
[137] restfulr_0.0.15