Last updated: 2019-09-14
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Knit directory: ptb_workflowr/
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Below is a dataframe with the top SNP at every locus, and the gene that is nearest to the top SNP. for each SNP I’ve included the torus
locus discovery fdr from several models (best, newfour, newnoeqtl, null).
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux
Matrix products: default
BLAS: /usr/lib/libopenblasp-r0.3.6.so
LAPACK: /usr/lib/liblapack.so.3.8.0
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_1.0.0.9000 ldshrink_1.0-1 furrr_0.1.0
[7] future_1.13.0 bigsnpr_0.11.5 bigstatsr_0.9.9
[10] vroom_1.0.1 RSQLite_2.1.1.9003 drake_7.4.0.9000
[13] fs_1.3.1 susieR_0.8.1.0521 here_0.1
[16] dbplyr_1.4.0 MonetDBLite_0.6.1 glue_1.3.1
[19] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3
[22] purrr_0.3.2 readr_1.3.1 tidyr_0.8.3
[25] tibble_2.1.3 ggplot2_3.2.1 tidyverse_1.2.1.9000
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 RcppEigen_0.3.3.5.0
[3] rprojroot_1.3-2 XVector_0.22.0
[5] GenomicRanges_1.34.0 rstudioapi_0.10
[7] listenv_0.7.0 DT_0.6
[9] bit64_0.9-7 lubridate_1.7.4
[11] xml2_1.2.2 codetools_0.2-16
[13] knitr_1.23 zeallot_0.1.0
[15] jsonlite_1.6 workflowr_1.3.0.9000
[17] Rsamtools_1.34.1 broom_0.5.2
[19] shiny_1.3.2 compiler_3.6.1
[21] httr_1.4.0 backports_1.1.4
[23] assertthat_0.2.1 Matrix_1.2-17
[25] lazyeval_0.2.2 cli_1.1.0
[27] later_0.8.0 htmltools_0.3.6
[29] tools_3.6.1 igraph_1.2.4.1
[31] gtable_0.3.0 GenomeInfoDbData_1.2.0
[33] Rcpp_1.0.2 Biobase_2.44.0
[35] cellranger_1.1.0 vctrs_0.2.0
[37] Biostrings_2.50.2 nlme_3.1-140
[39] rtracklayer_1.42.2 crosstalk_1.0.0
[41] iterators_1.0.12 wavethresh_4.6.8
[43] xfun_0.7 globals_0.12.4
[45] plyranges_1.4.3 rvest_0.3.4
[47] mime_0.7 XML_3.98-1.20
[49] zlibbioc_1.28.0 MASS_7.3-51.4
[51] scales_1.0.0 promises_1.0.1
[53] hms_0.5.0 parallel_3.6.1
[55] SummarizedExperiment_1.12.0 yaml_2.2.0
[57] memoise_1.1.0 stringi_1.4.3
[59] S4Vectors_0.20.1 foreach_1.4.7
[61] BiocGenerics_0.30.0 BiocParallel_1.16.6
[63] storr_1.2.2 GenomeInfoDb_1.18.2
[65] rlang_0.4.0 pkgconfig_2.0.2
[67] bitops_1.0-6 matrixStats_0.54.0
[69] evaluate_0.14 lattice_0.20-38
[71] htmlwidgets_1.3 GenomicAlignments_1.18.1
[73] cowplot_1.0.0 bit_1.1-14
[75] magrittr_1.5 R6_2.4.0
[77] IRanges_2.16.0 generics_0.0.2
[79] base64url_1.4 DelayedArray_0.8.0
[81] DBI_1.0.0.9002 pillar_1.4.2
[83] haven_2.1.0 whisker_0.3-2
[85] withr_2.1.2 RCurl_1.95-4.12
[87] modelr_0.1.4 crayon_1.3.4
[89] rmarkdown_1.13 grid_3.6.1
[91] readxl_1.3.1 data.table_1.12.2
[93] blob_1.2.0 git2r_0.26.1
[95] reprex_0.3.0 digest_0.6.20
[97] xtable_1.8-4 httpuv_1.5.1
[99] RcppParallel_4.4.3 stats4_3.6.1
[101] munsell_0.5.0