Preliminary Enrichment Fine-mapping Results
Nicholas Knoblauch
2019-07-02
Last updated: 2019-07-10
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Knit directory: ptb_workflowr/
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The loci
The genome was broken in to 1703 regions (using Pickrell’s ldetect). Regions were broken into subregions if they contained greater than 21539 SNPs, unless this would result in a subregion with fewer than 50 SNPs. This means that region size varied from 49 SNPs to max(snp_range$snpct) SNPs. The functional enrichment program torus was run individually on each of the following features:
Warning in bind_rows_(x, .id): Unequal factor levels: coercing to characterWarning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector
Warning in bind_rows_(x, .id): binding character and factor vector,
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Warning in bind_rows_(x, .id): binding character and factor vector,
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Warning in bind_rows_(x, .id): binding character and factor vector,
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Warning in bind_rows_(x, .id): binding character and factor vector,
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Warning in bind_rows_(x, .id): binding character and factor vector,
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Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector
Warning in bind_rows_(x, .id): binding character and factor vector,
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Warning in bind_rows_(x, .id): binding character and factor vector,
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Warning in bind_rows_(x, .id): binding character and factor vector,
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Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vectorForward Selection
Four steps of forward selection were used to obtain a final multivariate model. In each step, the term that added the most to the joint likelihood was added to the model.
Fine mapping with susie was then run on the top 5 loci, after generating priors using torus. susie was run assuming 1 causal variant per locus.
Locus 1
The top hit is on chromosome 1.
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux
Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblas_haswellp-r0.3.6.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] tidyselect_0.2.5 RSSp_0.9.0.9000 ldmap_0.0.0.9000
[4] daprcpp_1.0 ldshrink_1.0-1 archive_1.0.0
[7] vroom_1.0.2.9000 RSQLite_2.1.1 glue_1.3.1
[10] drake_7.4.0.9000 fs_1.3.1 susieR_0.8.1.0525
[13] here_0.1 forcats_0.4.0 stringr_1.4.0
[16] dplyr_0.8.3 purrr_0.3.2 readr_1.3.1
[19] tidyr_0.8.3 tibble_2.1.3 ggplot2_3.2.0
[22] tidyverse_1.2.1 dbplyr_1.4.2 MonetDBLite_0.6.1
[25] DT_0.7
loaded via a namespace (and not attached):
[1] nlme_3.1-140 bitops_1.0-6 lubridate_1.7.4
[4] bit64_0.9-7 filelock_1.0.2 httr_1.4.0
[7] rprojroot_1.3-2 GenomeInfoDb_1.20.0 tools_3.6.1
[10] backports_1.1.4 R6_2.4.0 DBI_1.0.0
[13] lazyeval_0.2.2 BiocGenerics_0.30.0 colorspace_1.4-1
[16] wavethresh_4.6.8 withr_2.1.2 bit_1.1-14
[19] compiler_3.6.1 git2r_0.26.1 cli_1.1.0
[22] rvest_0.3.4 xml2_1.2.0 labeling_0.3
[25] scales_1.0.0 digest_0.6.20 txtq_0.1.3
[28] rmarkdown_1.13 XVector_0.24.0 pkgconfig_2.0.2
[31] htmltools_0.3.6 htmlwidgets_1.3 rlang_0.4.0.9000
[34] readxl_1.3.1 rstudioapi_0.10 shiny_1.3.2
[37] generics_0.0.2 jsonlite_1.6 crosstalk_1.0.0
[40] RCurl_1.95-4.12 magrittr_1.5 GenomeInfoDbData_1.2.1
[43] Matrix_1.2-17 Rcpp_1.0.1 munsell_0.5.0
[46] S4Vectors_0.22.0 stringi_1.4.3 whisker_0.3-2
[49] yaml_2.2.0 MASS_7.3-51.4 storr_1.2.2
[52] zlibbioc_1.30.0 grid_3.6.1 blob_1.1.1
[55] promises_1.0.1 parallel_3.6.1 crayon_1.3.4
[58] lattice_0.20-38 haven_2.1.0 hms_0.4.2
[61] knitr_1.23 pillar_1.4.2 igraph_1.2.4.1
[64] GenomicRanges_1.36.0 base64url_1.4 codetools_0.2-16
[67] stats4_3.6.1 evaluate_0.14 RcppParallel_4.4.3
[70] modelr_0.1.4 httpuv_1.5.1 cellranger_1.1.0
[73] gtable_0.3.0 assertthat_0.2.1 xfun_0.7
[76] mime_0.7 xtable_1.8-4 RcppEigen_0.3.3.5.0
[79] broom_0.5.2 later_0.8.0 memoise_1.1.0
[82] IRanges_2.18.1 workflowr_1.4.0