Comparing predictdb & Munro: predictdb eQTL + sQTL + Munro rsQTL + apaQTL VS all 8 weights
XSun
2024-09-09
Last updated: 2024-09-09
Checks: 6 1
Knit directory: multigroup_ctwas_analysis/
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Settings
6 modalities from Munro
- Weight processing:
PredictDB:
all the PredictDB are converted from FUSION weights
- drop_strand_ambig = TRUE,
- scale_by_ld_variance = F (FUSION converted weights)
- load_predictdb_LD = F,
- Parameter estimation and fine-mapping
- niter_prefit = 5,
- niter = 30(default),
- L: determined by uniform susie,
- group_prior_var_structure = “shared_type”,
- maxSNP = 20000,
- min_nonSNP_PIP = 0.5,
weights from predictdb
- Weight processing:
PredictDB (eqtl, sqtl)
- drop_strand_ambig = TRUE,
- scale_by_ld_variance = T
- load_predictdb_LD = F,
- Parameter estimation and fine-mapping
- group_prior_var_structure = “shared_type”,
- filter_L = TRUE,
- filter_nonSNP_PIP = FALSE,
- min_nonSNP_PIP = 0.5,
- min_abs_corr = 0.1,
mem: 100g 5cores
Results
Four weights
predictdb eQTL + sQTL + Munro rsQTL + apaQTL
2024-09-09 14:16:06 INFO::Annotating ctwas finemapping result ...
2024-09-09 14:16:17 INFO::add gene_name and gene_type
2024-09-09 14:16:18 INFO::split PIPs for traits mapped to multiple genes
2024-09-09 14:16:19 INFO::use gene mid positions
2024-09-09 14:16:19 INFO::add SNP positionsEight weights
predictdb eQTL + sQTL + Munro 6 modalities
2024-09-09 14:16:47 INFO::Annotating ctwas finemapping result ...
2024-09-09 14:16:52 INFO::add gene_name and gene_typeWarning in left_join(., gene_annot, by = "gene_id", multiple = "all"): Detected an unexpected many-to-many relationship between `x` and `y`.
i Row 185 of `x` matches multiple rows in `y`.
i Row 3411 of `y` matches multiple rows in `x`.
i If a many-to-many relationship is expected, set `relationship =
"many-to-many"` to silence this warning.2024-09-09 14:16:52 INFO::split PIPs for traits mapped to multiple genes
2024-09-09 14:16:53 INFO::use gene mid positions
2024-09-09 14:16:53 INFO::add SNP positions
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] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.1 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[5] readr_2.1.2 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.5.1
[9] tidyverse_1.3.1 data.table_1.14.2 logging_0.10-108 ctwas_0.4.11
loaded via a namespace (and not attached):
[1] colorspace_2.0-3 rjson_0.2.21
[3] ellipsis_0.3.2 rprojroot_2.0.3
[5] XVector_0.36.0 locuszoomr_0.2.1
[7] GenomicRanges_1.48.0 fs_1.5.2
[9] rstudioapi_0.13 farver_2.1.0
[11] DT_0.22 ggrepel_0.9.1
[13] bit64_4.0.5 lubridate_1.8.0
[15] AnnotationDbi_1.58.0 fansi_1.0.3
[17] xml2_1.3.3 codetools_0.2-18
[19] cachem_1.0.6 knitr_1.39
[21] jsonlite_1.8.0 workflowr_1.7.0
[23] Rsamtools_2.12.0 broom_0.8.0
[25] dbplyr_2.1.1 png_0.1-7
[27] compiler_4.2.0 httr_1.4.3
[29] backports_1.4.1 assertthat_0.2.1
[31] Matrix_1.5-3 fastmap_1.1.0
[33] lazyeval_0.2.2 cli_3.6.1
[35] later_1.3.0 htmltools_0.5.2
[37] prettyunits_1.1.1 tools_4.2.0
[39] gtable_0.3.0 glue_1.6.2
[41] GenomeInfoDbData_1.2.8 rappdirs_0.3.3
[43] Rcpp_1.0.12 Biobase_2.56.0
[45] cellranger_1.1.0 jquerylib_0.1.4
[47] vctrs_0.6.5 Biostrings_2.64.0
[49] rtracklayer_1.56.0 crosstalk_1.2.0
[51] xfun_0.41 rvest_1.0.2
[53] lifecycle_1.0.4 irlba_2.3.5
[55] restfulr_0.0.14 ensembldb_2.20.2
[57] XML_3.99-0.14 zlibbioc_1.42.0
[59] zoo_1.8-10 scales_1.3.0
[61] gggrid_0.2-0 hms_1.1.1
[63] promises_1.2.0.1 MatrixGenerics_1.8.0
[65] ProtGenerics_1.28.0 parallel_4.2.0
[67] SummarizedExperiment_1.26.1 AnnotationFilter_1.20.0
[69] LDlinkR_1.2.3 yaml_2.3.5
[71] curl_4.3.2 memoise_2.0.1
[73] sass_0.4.1 biomaRt_2.54.1
[75] stringi_1.7.6 RSQLite_2.3.1
[77] highr_0.9 S4Vectors_0.34.0
[79] BiocIO_1.6.0 GenomicFeatures_1.48.3
[81] BiocGenerics_0.42.0 filelock_1.0.2
[83] BiocParallel_1.30.3 GenomeInfoDb_1.39.9
[85] rlang_1.1.2 pkgconfig_2.0.3
[87] matrixStats_0.62.0 bitops_1.0-7
[89] evaluate_0.15 lattice_0.20-45
[91] labeling_0.4.2 GenomicAlignments_1.32.0
[93] htmlwidgets_1.5.4 cowplot_1.1.1
[95] bit_4.0.4 tidyselect_1.2.0
[97] magrittr_2.0.3 R6_2.5.1
[99] IRanges_2.30.0 generics_0.1.2
[101] DelayedArray_0.22.0 DBI_1.2.2
[103] withr_2.5.0 haven_2.5.0
[105] pgenlibr_0.3.3 pillar_1.9.0
[107] KEGGREST_1.36.3 RCurl_1.98-1.7
[109] mixsqp_0.3-43 modelr_0.1.8
[111] crayon_1.5.1 utf8_1.2.2
[113] BiocFileCache_2.4.0 plotly_4.10.0
[115] tzdb_0.4.0 rmarkdown_2.25
[117] progress_1.2.2 readxl_1.4.0
[119] grid_4.2.0 blob_1.2.3
[121] git2r_0.30.1 reprex_2.0.1
[123] digest_0.6.29 httpuv_1.6.5
[125] stats4_4.2.0 munsell_0.5.0
[127] viridisLite_0.4.0 bslib_0.3.1