real data coloc analysis
2024-10-22
Last updated: 2025-04-11
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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Method
- For each trait, select regions with at lease one high PIP expression/splicing trait (PIP>0.8)
- based on multi-cTWAS results with three molecular traits (eQTL,sQTL,stQTL) from five tissues.
- Run coloc with eQTL and sQTL full summary statistics from five tissues
- no stQTL full summary statistics
- Comparing the number of expression and splicing molecular traits identified by coloc (PP4>0.8), single-cTWAS (PIP>0.8) and multi-cTWAS (PIP>0.8)
- don’t include stability traits identified by multi-cTWAS
2025-04-11 14:03:08 INFO::Annotating susie alpha result ...
2025-04-11 14:03:08 INFO::Map molecular traits to genes
2025-04-11 14:03:10 INFO::Split PIPs for molecular traits mapped to multiple genes2025-04-11 14:03:43 INFO::Annotating susie alpha result ...
2025-04-11 14:03:47 INFO::Map molecular traits to genes
2025-04-11 14:03:49 INFO::Split PIPs for molecular traits mapped to multiple genes2025-04-11 14:04:18 INFO::Annotating susie alpha result ...
2025-04-11 14:04:18 INFO::Map molecular traits to genes
2025-04-11 14:04:20 INFO::Split PIPs for molecular traits mapped to multiple genes2025-04-11 14:04:38 INFO::Annotating susie alpha result ...
2025-04-11 14:04:38 INFO::Map molecular traits to genes
2025-04-11 14:04:39 INFO::Split PIPs for molecular traits mapped to multiple genes2025-04-11 14:04:52 INFO::Annotating susie alpha result ...
2025-04-11 14:04:52 INFO::Map molecular traits to genes
2025-04-11 14:04:53 INFO::Split PIPs for molecular traits mapped to multiple genesnumber of genes identified by each method
compare number of genes per locus
compare number of genes per locus (locus with multi-ctwas signals)
number of molecular traits identified by each method
compare number of molecular traits per locus
compare number of molecular traits per locus (locus with multi-ctwas signals)
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 pheatmap_1.0.12
[13] magrittr_2.0.3 RSQLite_2.3.7
[15] lubridate_1.9.3 forcats_1.0.0
[17] stringr_1.5.1 dplyr_1.1.4
[19] purrr_1.0.2 readr_2.1.5
[21] tidyr_1.3.1 tibble_3.2.1
[23] tidyverse_2.0.0 ctwas_0.5.5.9001
[25] data.table_1.16.0 gridExtra_2.3
[27] ggVennDiagram_1.5.2 ggplot2_3.5.1
[29] 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 compiler_4.2.0
[23] httr_1.4.7 Matrix_1.5-3
[25] fastmap_1.2.0 lazyeval_0.2.2
[27] cli_3.6.3 later_1.3.2
[29] htmltools_0.5.8.1 prettyunits_1.2.0
[31] tools_4.2.0 gtable_0.3.5
[33] glue_1.7.0 GenomeInfoDbData_1.2.9
[35] rappdirs_0.3.3 Rcpp_1.0.13
[37] jquerylib_0.1.4 vctrs_0.6.5
[39] Biostrings_2.66.0 rtracklayer_1.58.0
[41] xfun_0.47 ps_1.7.1
[43] timechange_0.3.0 irlba_2.3.5.1
[45] lifecycle_1.0.4 restfulr_0.0.15
[47] XML_3.99-0.14 zoo_1.8-12
[49] getPass_0.2-2 zlibbioc_1.44.0
[51] scales_1.3.0 gggrid_0.2-0
[53] hms_1.1.3 promises_1.3.0
[55] MatrixGenerics_1.10.0 ProtGenerics_1.30.0
[57] parallel_4.2.0 SummarizedExperiment_1.28.0
[59] RColorBrewer_1.1-3 LDlinkR_1.4.0
[61] yaml_2.3.10 curl_5.2.3
[63] memoise_2.0.1 sass_0.4.9
[65] biomaRt_2.54.1 stringi_1.8.4
[67] highr_0.11 BiocIO_1.8.0
[69] filelock_1.0.3 BiocParallel_1.32.6
[71] repr_1.1.4 rlang_1.1.4
[73] pkgconfig_2.0.3 matrixStats_1.4.1
[75] bitops_1.0-8 evaluate_1.0.0
[77] lattice_0.20-45 labeling_0.4.3
[79] GenomicAlignments_1.34.1 htmlwidgets_1.6.4
[81] cowplot_1.1.3 bit_4.5.0
[83] processx_3.7.0 tidyselect_1.2.1
[85] AMR_2.1.1 R6_2.5.1
[87] generics_0.1.3 DelayedArray_0.24.0
[89] DBI_1.2.3 pgenlibr_0.3.7
[91] pillar_1.9.0 whisker_0.4
[93] withr_3.0.1 mixsqp_0.3-54
[95] KEGGREST_1.38.0 RCurl_1.98-1.16
[97] crayon_1.5.3 utf8_1.2.4
[99] BiocFileCache_2.6.1 plotly_4.10.4
[101] tzdb_0.4.0 rmarkdown_2.28
[103] progress_1.2.3 grid_4.2.0
[105] blob_1.2.4 callr_3.7.2
[107] git2r_0.30.1 digest_0.6.37
[109] httpuv_1.6.5 munsell_0.5.1
[111] viridisLite_0.4.2 skimr_2.1.4
[113] bslib_0.8.0