simulation_no_enrichment
2024-2-13
Last updated: 2025-03-06
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 597b26f | sq-96 | 2025-03-06 | update |
| html | 597b26f | sq-96 | 2025-03-06 | update |
One tissue simulation
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'data.table'The following objects are masked from 'package:dplyr':
between, first, lastggbreak v0.1.2
If you use ggbreak in published research, please cite the following
paper:
S Xu, M Chen, T Feng, L Zhan, L Zhou, G Yu. Use ggbreak to effectively
utilize plotting space to deal with large datasets and outliers.
Frontiers in Genetics. 2021, 12:774846. doi: 10.3389/fgene.2021.774846
Attaching package: 'gridExtra'The following object is masked from 'package:dplyr':
combine
Attaching package: 'cowplot'The following object is masked from 'package:ggpubr':
get_legend------------------------------------------------------------------------------You have loaded plyr after dplyr - this is likely to cause problems.
If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
library(plyr); library(dplyr)------------------------------------------------------------------------------
Attaching package: 'plyr'The following object is masked from 'package:ggpubr':
mutateThe following objects are masked from 'package:dplyr':
arrange, count, desc, failwith, id, mutate, rename, summarise,
summarizeEnrichment=1 (same variance=10)
gene prior = 2.5e-4, snp prior = 2.5e-4, gene variance = 10, snp variance = 10, gene pve=0.001974, snp pve=0.3
Enrichment (G-test,min_p=0.8,min_gene=1)
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
| Version | Author | Date |
|---|---|---|
| 597b26f | sq-96 | 2025-03-06 |
Enrichment (F-test,min_p=0.8,min_gene=1)
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
| Version | Author | Date |
|---|---|---|
| 597b26f | sq-96 | 2025-03-06 |
Enrichment (G-test,min_p=0,min_gene=1)
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
| Version | Author | Date |
|---|---|---|
| 597b26f | sq-96 | 2025-03-06 |
Enrichment (F-test,min_p=0,min_gene=1)
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
| Version | Author | Date |
|---|---|---|
| 597b26f | sq-96 | 2025-03-06 |
Enrichment (G-test,min_p=0,min_gene=0)
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
| Version | Author | Date |
|---|---|---|
| 597b26f | sq-96 | 2025-03-06 |
Enrichment (F-test,min_p=0,min_gene=0)
Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
Removed 1 row containing missing values or values outside the scale range
(`geom_point()`).
| Version | Author | Date |
|---|---|---|
| 597b26f | sq-96 | 2025-03-06 |
Enrichment=1 (same variance=20)
gene prior = 2.5e-4, snp prior = 2.5e-4, gene variance = 10, snp variance = 10, gene pve=0.003948, snp pve=0.3
Enrichment=1 (same variance=40)
gene prior = 2.5e-4, snp prior = 2.5e-4, gene variance = 10, snp variance = 10, gene pve=0.007896, snp pve=0.3
Enrichment=1 (same variance=80)
gene prior = 2.5e-4, snp prior = 2.5e-4, gene variance = 10, snp variance = 10, gene pve=0.015792, snp pve=0.3
Enrichment (F-test,min_p=0,min_gene=0)
| Version | Author | Date |
|---|---|---|
| 597b26f | sq-96 | 2025-03-06 |
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 gridExtra_2.3
[5] ggpubr_0.6.0 ggbreak_0.1.2 data.table_1.16.0 ggplot2_3.5.1
[9] dplyr_1.1.4 tidyr_1.3.1 ctwas_0.5.4.9000 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] backports_1.4.1 BiocFileCache_2.6.1
[3] repr_1.1.4 lazyeval_0.2.2
[5] BiocParallel_1.32.6 GenomeInfoDb_1.34.9
[7] LDlinkR_1.4.0 digest_0.6.37
[9] yulab.utils_0.1.7 ensembldb_2.22.0
[11] htmltools_0.5.8.1 fansi_1.0.6
[13] magrittr_2.0.3 memoise_2.0.1
[15] tzdb_0.4.0 Biostrings_2.66.0
[17] readr_2.1.5 AMR_2.1.1
[19] matrixStats_1.4.1 locuszoomr_0.3.5
[21] prettyunits_1.2.0 colorspace_2.1-1
[23] skimr_2.1.4 blob_1.2.4
[25] rappdirs_0.3.3 ggrepel_0.9.6
[27] xfun_0.47 callr_3.7.2
[29] crayon_1.5.3 RCurl_1.98-1.16
[31] jsonlite_1.8.9 zoo_1.8-12
[33] glue_1.7.0 gtable_0.3.5
[35] zlibbioc_1.44.0 XVector_0.38.0
[37] DelayedArray_0.24.0 car_3.1-1
[39] BiocGenerics_0.44.0 abind_1.4-5
[41] scales_1.3.0 DBI_1.2.3
[43] rstatix_0.7.2 Rcpp_1.0.13
[45] viridisLite_0.4.2 progress_1.2.3
[47] gridGraphics_0.5-1 bit_4.5.0
[49] stats4_4.2.0 htmlwidgets_1.6.4
[51] httr_1.4.7 pkgconfig_2.0.3
[53] XML_3.99-0.14 farver_2.1.2
[55] sass_0.4.9 dbplyr_2.5.0
[57] utf8_1.2.4 labeling_0.4.3
[59] ggplotify_0.1.2 tidyselect_1.2.1
[61] rlang_1.1.4 later_1.3.2
[63] AnnotationDbi_1.60.2 munsell_0.5.1
[65] pgenlibr_0.3.7 tools_4.2.0
[67] cachem_1.1.0 cli_3.6.3
[69] generics_0.1.3 RSQLite_2.3.7
[71] broom_1.0.5 evaluate_1.0.0
[73] stringr_1.5.1 fastmap_1.2.0
[75] yaml_2.3.10 processx_3.7.0
[77] knitr_1.48 bit64_4.5.2
[79] fs_1.6.4 purrr_1.0.2
[81] KEGGREST_1.38.0 AnnotationFilter_1.22.0
[83] whisker_0.4 aplot_0.2.3
[85] xml2_1.3.3 biomaRt_2.54.1
[87] compiler_4.2.0 rstudioapi_0.14
[89] plotly_4.10.4 filelock_1.0.3
[91] curl_5.2.3 png_0.1-7
[93] ggsignif_0.6.3 tibble_3.2.1
[95] bslib_0.8.0 stringi_1.8.4
[97] highr_0.11 ps_1.7.1
[99] GenomicFeatures_1.50.4 lattice_0.20-45
[101] ProtGenerics_1.30.0 Matrix_1.5-3
[103] vctrs_0.6.5 pillar_1.9.0
[105] lifecycle_1.0.4 jquerylib_0.1.4
[107] bitops_1.0-8 irlba_2.3.5.1
[109] httpuv_1.6.5 patchwork_1.3.0
[111] rtracklayer_1.58.0 GenomicRanges_1.50.2
[113] R6_2.5.1 BiocIO_1.8.0
[115] promises_1.3.0 IRanges_2.32.0
[117] codetools_0.2-18 SummarizedExperiment_1.28.0
[119] rprojroot_2.0.3 rjson_0.2.23
[121] withr_3.0.1 GenomicAlignments_1.34.1
[123] Rsamtools_2.14.0 S4Vectors_0.36.2
[125] GenomeInfoDbData_1.2.9 parallel_4.2.0
[127] hms_1.1.3 grid_4.2.0
[129] ggfun_0.1.6 gggrid_0.2-0
[131] rmarkdown_2.28 carData_3.0-5
[133] MatrixGenerics_1.10.0 logging_0.10-108
[135] git2r_0.30.1 mixsqp_0.3-54
[137] getPass_0.2-2 Biobase_2.58.0
[139] base64enc_0.1-3 restfulr_0.0.15