real data coloc analysis
2024-10-22
Last updated: 2025-05-20
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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| Rmd | 8130e97 | sq-96 | 2025-05-20 | update |
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| Rmd | 56aa1a4 | sq-96 | 2025-05-19 | update |
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| Rmd | c327808 | sq-96 | 2025-05-17 | update |
| Rmd | ae857ab | sq-96 | 2025-05-15 | update |
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| Rmd | 215445c | sq-96 | 2025-04-21 | update |
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| Rmd | 2fa6d8b | sq-96 | 2025-04-16 | update |
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SCZ one QTL
Warning in brewer.pal(n = max(lengths(list(prop1, prop2, prop3))), name = "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
SCZ two QTLs
SCZ three QTLs
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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] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.22.0
[3] AnnotationFilter_1.22.0 GenomicFeatures_1.50.4
[5] AnnotationDbi_1.60.2 Biobase_2.58.0
[7] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[9] IRanges_2.32.0 S4Vectors_0.36.2
[11] BiocGenerics_0.44.0 data.table_1.16.0
[13] ctwas_0.5.20 RColorBrewer_1.1-3
[15] workflowr_1.7.0
loaded via a namespace (and not attached):
[1] colorspace_2.1-1 rjson_0.2.23
[3] rprojroot_2.0.3 XVector_0.38.0
[5] locuszoomr_0.3.5 base64enc_0.1-3
[7] fs_1.6.4 rstudioapi_0.14
[9] farver_2.1.2 ggrepel_0.9.6
[11] bit64_4.5.2 fansi_1.0.6
[13] xml2_1.3.3 logging_0.10-108
[15] codetools_0.2-18 cachem_1.1.0
[17] knitr_1.48 jsonlite_1.8.9
[19] Rsamtools_2.14.0 dbplyr_2.5.0
[21] png_0.1-7 readr_2.1.5
[23] compiler_4.2.0 httr_1.4.7
[25] Matrix_1.5-3 fastmap_1.2.0
[27] lazyeval_0.2.2 cli_3.6.3
[29] later_1.3.2 htmltools_0.5.8.1
[31] prettyunits_1.2.0 tools_4.2.0
[33] gtable_0.3.5 glue_1.7.0
[35] GenomeInfoDbData_1.2.9 dplyr_1.1.4
[37] rappdirs_0.3.3 Rcpp_1.0.13
[39] jquerylib_0.1.4 vctrs_0.6.5
[41] Biostrings_2.66.0 rtracklayer_1.58.0
[43] xfun_0.47 stringr_1.5.1
[45] ps_1.7.1 irlba_2.3.5.1
[47] lifecycle_1.0.4 restfulr_0.0.15
[49] XML_3.99-0.14 zoo_1.8-12
[51] getPass_0.2-2 zlibbioc_1.44.0
[53] scales_1.3.0 gggrid_0.2-0
[55] hms_1.1.3 promises_1.3.0
[57] MatrixGenerics_1.10.0 ProtGenerics_1.30.0
[59] parallel_4.2.0 SummarizedExperiment_1.28.0
[61] LDlinkR_1.4.0 yaml_2.3.10
[63] curl_5.2.3 memoise_2.0.1
[65] ggplot2_3.5.1 sass_0.4.9
[67] biomaRt_2.54.1 stringi_1.8.4
[69] RSQLite_2.3.7 highr_0.11
[71] BiocIO_1.8.0 filelock_1.0.3
[73] BiocParallel_1.32.6 repr_1.1.4
[75] rlang_1.1.4 pkgconfig_2.0.3
[77] bitops_1.0-8 matrixStats_1.4.1
[79] evaluate_1.0.0 lattice_0.20-45
[81] purrr_1.0.2 labeling_0.4.3
[83] GenomicAlignments_1.34.1 htmlwidgets_1.6.4
[85] cowplot_1.1.3 bit_4.5.0
[87] processx_3.7.0 tidyselect_1.2.1
[89] magrittr_2.0.3 AMR_2.1.1
[91] R6_2.5.1 generics_0.1.3
[93] DelayedArray_0.24.0 DBI_1.2.3
[95] withr_3.0.1 pgenlibr_0.3.7
[97] pillar_1.9.0 whisker_0.4
[99] mixsqp_0.3-54 KEGGREST_1.38.0
[101] RCurl_1.98-1.16 tibble_3.2.1
[103] crayon_1.5.3 utf8_1.2.4
[105] BiocFileCache_2.6.1 plotly_4.10.4
[107] tzdb_0.4.0 rmarkdown_2.28
[109] progress_1.2.3 grid_4.2.0
[111] blob_1.2.4 callr_3.7.2
[113] git2r_0.30.1 digest_0.6.37
[115] tidyr_1.3.1 httpuv_1.6.5
[117] munsell_0.5.1 viridisLite_0.4.2
[119] skimr_2.1.4 bslib_0.8.0