Last updated: 2021-03-05
Checks: 6 1
Knit directory: PSYMETAB/
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Ignored files:
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Untracked files:
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Unstaged changes:
Modified: analysis/genetic_quality_control.Rmd
Modified: cache_log.csv
Modified: post_impute.log
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 02aac58 | Jenny Sjaarda | 2021-03-05 | Update plans Rmd |
| html | 1a38b84 | Jenny Sjaarda | 2021-03-04 | Build site. |
| html | 8331ac1 | Jenny Sjaarda | 2021-03-04 | Build site. |
| html | 3ce6d16 | Jenny Sjaarda | 2021-03-04 | Build site. |
| Rmd | dab6add | Jenny Sjaarda | 2021-03-04 | Building plans Rmd |
| html | b4487b7 | Jenny Sjaarda | 2021-03-03 | Build site. |
| Rmd | 0304998 | Jenny Sjaarda | 2021-03-03 | testing genetics_qc |
| Rmd | 13aa9db | jennysjaarda | 2021-03-03 | misc updates to website Rmd pages |
| Rmd | 941b66d | Jenny Sjaarda | 2021-03-02 | add new Rmd files and respective html files |
| html | 941b66d | Jenny Sjaarda | 2021-03-02 | add new Rmd files and respective html files |
drake was used to manage all workflows. See plan.R and functions.R for code.
outdated(qc_prep)character(0)vis_drake_graph(qc_prep, main="QC preparation drake plan")outdated(pre_impute_qc)character(0)vis_drake_graph(pre_impute_qc, main="Pre-imputation drake plan")outdated(download_impute)character(0)vis_drake_graph(download_impute, main="Download imputed data drake plan")outdated(post_impute)character(0)vis_drake_graph(post_impute, main="Post-imputation quality control drake plan")outdated(analysis_prep)character(0)vis_drake_graph(analysis_prep, main="Analysis prep drake plan")outdated(init_analysis)character(0)vis_drake_graph(init_analysis, main="Initial analysis drake plan")#outdated(ukbb_analysis)
#vis_drake_graph(ukbb_analysis, main="UKBB analysis drake plan")outdated(process_init)[1] "bgenie_merge" "bgenie_unzip"
[3] "psy_ukbb_merge" "psy_ukbb_merge_AF"
[5] "psy_ukbb_merge_AF_prune" "ukbb_geno"
[7] "ukbb_top_snps_chr" "write_ukbb_comparison" vis_drake_graph(process_init, main="Process initial analysis drake plan")
sessionInfo()R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /data/sgg2/jenny/bin/R-3.5.3/lib64/R/lib/libRblas.so
LAPACK: /data/sgg2/jenny/bin/R-3.5.3/lib64/R/lib/libRlapack.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 rbgen_0.1 ukbtools_0.11.3
[4] hrbrthemes_0.8.0 OpenImageR_1.1.6 fuzzyjoin_0.1.5
[7] kableExtra_1.1.0 R.utils_2.9.2 R.oo_1.23.0
[10] R.methodsS3_1.7.1 TwoSampleMR_0.4.25 reader_1.0.6
[13] NCmisc_1.1.6 optparse_1.6.4 readxl_1.3.1
[16] ggthemes_4.2.0 tryCatchLog_1.1.6 futile.logger_1.4.3
[19] DataExplorer_0.8.0 taRifx_1.0.6.1 qqman_0.1.4
[22] MASS_7.3-51.5 bit64_0.9-7 bit_1.1-14
[25] rslurm_0.5.0 rmeta_3.0 devtools_2.2.1
[28] usethis_1.5.1 data.table_1.12.8 clustermq_0.8.8.1
[31] future.batchtools_0.8.1 future_1.15.1 rlang_0.4.5
[34] knitr_1.26 drake_7.12.0.9000 forcats_0.4.0
[37] stringr_1.4.0 dplyr_0.8.3 purrr_0.3.3
[40] readr_1.3.1 tidyr_1.0.3 tibble_2.1.3
[43] ggplot2_3.3.2 tidyverse_1.3.0 pacman_0.5.1
[46] processx_3.4.1 workflowr_1.6.0
loaded via a namespace (and not attached):
[1] backports_1.1.6 systemfonts_0.2.3 plyr_1.8.5
[4] igraph_1.2.5 storr_1.2.1 listenv_0.8.0
[7] digest_0.6.25 foreach_1.4.7 htmltools_0.4.0
[10] tiff_0.1-5 fansi_0.4.1 magrittr_1.5
[13] checkmate_1.9.4 memoise_1.1.0 base64url_1.4
[16] doParallel_1.0.15 remotes_2.1.0 globals_0.12.5
[19] extrafont_0.17 modelr_0.1.5 extrafontdb_1.0
[22] prettyunits_1.1.0 jpeg_0.1-8.1 colorspace_1.4-1
[25] rvest_0.3.5 rappdirs_0.3.1 haven_2.2.0
[28] xfun_0.11 callr_3.4.0 crayon_1.3.4
[31] jsonlite_1.6 iterators_1.0.12 brew_1.0-6
[34] glue_1.4.0 gtable_0.3.0 webshot_0.5.2
[37] pkgbuild_1.0.6 Rttf2pt1_1.3.8 scales_1.1.0
[40] futile.options_1.0.1 DBI_1.1.0 Rcpp_1.0.3
[43] xtable_1.8-4 viridisLite_0.3.0 progress_1.2.2
[46] txtq_0.2.0 htmlwidgets_1.5.1 httr_1.4.1
[49] getopt_1.20.3 calibrate_1.7.5 ellipsis_0.3.0
[52] XML_3.98-1.20 pkgconfig_2.0.3 dbplyr_1.4.2
[55] reshape2_1.4.3 later_1.0.0 visNetwork_2.0.9
[58] munsell_0.5.0 cellranger_1.1.0 tools_3.5.3
[61] cli_2.0.1 generics_0.0.2 broom_0.5.3
[64] fastmap_1.0.1 evaluate_0.14 yaml_2.2.0
[67] fs_1.3.1 packrat_0.5.0 nlme_3.1-143
[70] mime_0.8 whisker_0.4 formatR_1.7
[73] proftools_0.99-2 xml2_1.2.2 compiler_3.5.3
[76] rstudioapi_0.10 png_0.1-7 filelock_1.0.2
[79] testthat_2.3.1 reprex_0.3.0 stringi_1.4.5
[82] highr_0.8 ps_1.3.0 desc_1.2.0
[85] gdtools_0.2.2 lattice_0.20-38 vctrs_0.2.4
[88] pillar_1.4.3 lifecycle_0.1.0 networkD3_0.4
[91] httpuv_1.5.2 R6_2.4.1 promises_1.1.0
[94] gridExtra_2.3 sessioninfo_1.1.1 codetools_0.2-16
[97] lambda.r_1.2.4 assertthat_0.2.1 pkgload_1.0.2
[100] rprojroot_1.3-2 withr_2.1.2 batchtools_0.9.12
[103] parallel_3.5.3 hms_0.5.3 grid_3.5.3
[106] rmarkdown_1.18 git2r_0.26.1 shiny_1.4.0
[109] lubridate_1.7.4