methylation_analysis
2024-10-22
Last updated: 2024-10-25
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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Fusion Lasso model of DNA methylation
I built lasso model of DNA methylation with FUSION for Whole Blood and Colon Transverse. Similar to meQTL mapping, for each CpG site, I extracted surrounding 50kb genptypes and train lasso models with cross validation. With heritability cutoff p<0.0001, I have about 16,000 and 48,000 CpG sites in whole blood and colon transverse. Among which, 5,000 and 40,000 CpG sites are also in QTL mapping. Colon have more overlaps than whole blood. The average cross-validation R2 for lasso in whole blood and colon transverse are 0.393 and 0.248 In the single QTL approach (qval < 0.001), we have 7,720 and 91,466 CpG sites.
| Version | Author | Date |
|---|---|---|
| 919465c | sq-96 | 2024-10-23 |
cTWAS parameters with methylation lasso models (50kb, h2 pvalue<0.00001)
Percent of heritability with methylation lasso models
Top cTWAS genes with methylation lasso models
2024-10-25 13:47:16 INFO::Annotating susie alpha result ...
2024-10-25 13:47:16 INFO::Map molecular traits to genes
2024-10-25 13:47:20 INFO::Split PIPs for molecular traits mapped to multiple genescTWAS parameters with methylation lasso models (500kb, h2 pvalue<0.0001)
Percent of heritability with methylation lasso models
Top cTWAS genes with methylation lasso models
2024-10-25 13:47:33 INFO::Annotating susie alpha result ...
2024-10-25 13:47:33 INFO::Map molecular traits to genes
2024-10-25 13:47:34 INFO::Split PIPs for molecular traits mapped to multiple genescTWAS parameters with methylation single QTL models
### Percent of heritability with methylation single QTL models 
Top cTWAS genes with methylation single QTL models
2024-10-25 13:47:47 INFO::Annotating susie alpha result ...
2024-10-25 13:47:47 INFO::Map molecular traits to genes
2024-10-25 13:47:50 INFO::Split PIPs for molecular traits mapped to multiple genes
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] pheatmap_1.0.12 magrittr_2.0.3 RSQLite_2.3.7
[4] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[7] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5
[10] tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0
[13] ctwas_0.4.15 data.table_1.16.0 gridExtra_2.3
[16] ggVennDiagram_1.5.2 ggplot2_3.5.1 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 GenomicRanges_1.50.2
[7] fs_1.6.4 rstudioapi_0.14
[9] farver_2.1.2 DT_0.22
[11] ggrepel_0.9.6 bit64_4.5.2
[13] AnnotationDbi_1.60.2 fansi_1.0.6
[15] xml2_1.3.3 logging_0.10-108
[17] codetools_0.2-18 cachem_1.1.0
[19] knitr_1.48 jsonlite_1.8.9
[21] Rsamtools_2.14.0 dbplyr_2.5.0
[23] png_0.1-7 compiler_4.2.0
[25] httr_1.4.7 Matrix_1.5-3
[27] fastmap_1.2.0 lazyeval_0.2.2
[29] cli_3.6.3 later_1.3.2
[31] htmltools_0.5.8.1 prettyunits_1.2.0
[33] tools_4.2.0 gtable_0.3.5
[35] glue_1.7.0 GenomeInfoDbData_1.2.9
[37] rappdirs_0.3.3 Rcpp_1.0.13
[39] Biobase_2.58.0 jquerylib_0.1.4
[41] vctrs_0.6.5 Biostrings_2.66.0
[43] rtracklayer_1.58.0 crosstalk_1.2.1
[45] xfun_0.47 ps_1.7.1
[47] timechange_0.3.0 irlba_2.3.5.1
[49] lifecycle_1.0.4 restfulr_0.0.15
[51] ensembldb_2.22.0 XML_3.99-0.14
[53] getPass_0.2-2 zlibbioc_1.44.0
[55] zoo_1.8-12 scales_1.3.0
[57] gggrid_0.2-0 hms_1.1.3
[59] promises_1.3.0 MatrixGenerics_1.10.0
[61] ProtGenerics_1.30.0 parallel_4.2.0
[63] SummarizedExperiment_1.28.0 RColorBrewer_1.1-3
[65] AnnotationFilter_1.22.0 LDlinkR_1.4.0
[67] yaml_2.3.10 curl_5.2.3
[69] memoise_2.0.1 sass_0.4.9
[71] biomaRt_2.54.1 stringi_1.8.4
[73] highr_0.11 S4Vectors_0.36.2
[75] BiocIO_1.8.0 GenomicFeatures_1.50.4
[77] BiocGenerics_0.44.0 filelock_1.0.3
[79] BiocParallel_1.32.6 GenomeInfoDb_1.34.9
[81] rlang_1.1.4 pkgconfig_2.0.3
[83] matrixStats_1.4.1 bitops_1.0-8
[85] evaluate_1.0.0 lattice_0.20-45
[87] labeling_0.4.3 GenomicAlignments_1.34.1
[89] htmlwidgets_1.6.4 cowplot_1.1.3
[91] bit_4.5.0 processx_3.7.0
[93] tidyselect_1.2.1 R6_2.5.1
[95] IRanges_2.32.0 generics_0.1.3
[97] DelayedArray_0.24.0 DBI_1.2.3
[99] pgenlibr_0.3.7 pillar_1.9.0
[101] whisker_0.4 withr_3.0.1
[103] mixsqp_0.3-54 KEGGREST_1.38.0
[105] RCurl_1.98-1.16 crayon_1.5.3
[107] utf8_1.2.4 BiocFileCache_2.6.1
[109] plotly_4.10.4 tzdb_0.4.0
[111] rmarkdown_2.28 progress_1.2.3
[113] grid_4.2.0 blob_1.2.4
[115] callr_3.7.2 git2r_0.30.1
[117] digest_0.6.37 httpuv_1.6.5
[119] stats4_4.2.0 munsell_0.5.1
[121] viridisLite_0.4.2 bslib_0.8.0