Last updated: 2025-01-10

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Rmd 4731bfe sq-96 2024-12-02 update
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Method

  1. 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.
  1. Run coloc with eQTL and sQTL full summary statistics from five tissues
  • no stQTL full summary statistics
  1. 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
Loading required package: ensembldb
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Attaching package: 'BiocGenerics'
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    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
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Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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2025-01-10 11:47:40 INFO::Annotating fine-mapping result ...
2025-01-10 11:47:41 INFO::Map molecular traits to genes
2025-01-10 11:47:46 INFO::Drop 4078 unmapped molecular traits
2025-01-10 11:47:46 INFO::Split PIPs for molecular traits mapped to multiple genes
2025-01-10 11:47:56 INFO::Add gene positions
2025-01-10 11:47:57 INFO::Add SNP positions

LDL

Version Author Date
b12b348 sq-96 2024-12-02

WBC

SBP

SCZ

IBD


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_0.4.15             
[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            fs_1.6.4                   
  [7] rstudioapi_0.14             farver_2.1.2               
  [9] ggrepel_0.9.6               bit64_4.5.2                
 [11] fansi_1.0.6                 xml2_1.3.3                 
 [13] logging_0.10-108            codetools_0.2-18           
 [15] cachem_1.1.0                knitr_1.48                 
 [17] jsonlite_1.8.9              Rsamtools_2.14.0           
 [19] dbplyr_2.5.0                png_0.1-7                  
 [21] compiler_4.2.0              httr_1.4.7                 
 [23] Matrix_1.5-3                fastmap_1.2.0              
 [25] lazyeval_0.2.2              cli_3.6.3                  
 [27] later_1.3.2                 htmltools_0.5.8.1          
 [29] prettyunits_1.2.0           tools_4.2.0                
 [31] gtable_0.3.5                glue_1.7.0                 
 [33] GenomeInfoDbData_1.2.9      rappdirs_0.3.3             
 [35] Rcpp_1.0.13                 jquerylib_0.1.4            
 [37] vctrs_0.6.5                 Biostrings_2.66.0          
 [39] rtracklayer_1.58.0          xfun_0.47                  
 [41] ps_1.7.1                    timechange_0.3.0           
 [43] irlba_2.3.5.1               lifecycle_1.0.4            
 [45] restfulr_0.0.15             XML_3.99-0.14              
 [47] getPass_0.2-2               zlibbioc_1.44.0            
 [49] zoo_1.8-12                  scales_1.3.0               
 [51] gggrid_0.2-0                hms_1.1.3                  
 [53] promises_1.3.0              MatrixGenerics_1.10.0      
 [55] ProtGenerics_1.30.0         parallel_4.2.0             
 [57] SummarizedExperiment_1.28.0 RColorBrewer_1.1-3         
 [59] LDlinkR_1.4.0               yaml_2.3.10                
 [61] curl_5.2.3                  memoise_2.0.1              
 [63] sass_0.4.9                  biomaRt_2.54.1             
 [65] stringi_1.8.4               highr_0.11                 
 [67] BiocIO_1.8.0                filelock_1.0.3             
 [69] BiocParallel_1.32.6         rlang_1.1.4                
 [71] pkgconfig_2.0.3             matrixStats_1.4.1          
 [73] bitops_1.0-8                evaluate_1.0.0             
 [75] lattice_0.20-45             labeling_0.4.3             
 [77] GenomicAlignments_1.34.1    htmlwidgets_1.6.4          
 [79] cowplot_1.1.3               bit_4.5.0                  
 [81] processx_3.7.0              tidyselect_1.2.1           
 [83] R6_2.5.1                    generics_0.1.3             
 [85] DelayedArray_0.24.0         DBI_1.2.3                  
 [87] pgenlibr_0.3.7              pillar_1.9.0               
 [89] whisker_0.4                 withr_3.0.1                
 [91] mixsqp_0.3-54               KEGGREST_1.38.0            
 [93] RCurl_1.98-1.16             crayon_1.5.3               
 [95] utf8_1.2.4                  BiocFileCache_2.6.1        
 [97] plotly_4.10.4               tzdb_0.4.0                 
 [99] rmarkdown_2.28              progress_1.2.3             
[101] grid_4.2.0                  blob_1.2.4                 
[103] callr_3.7.2                 git2r_0.30.1               
[105] digest_0.6.37               httpuv_1.6.5               
[107] munsell_0.5.1               viridisLite_0.4.2          
[109] bslib_0.8.0