Last updated: 2019-09-04
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Knit directory: ptb_workflowr/
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| Rmd | 30bd2f7 | CreRecombinase | 2019-09-04 | wflow_publish(“analysis/region_discovery.Rmd”) |
library(tidyverse)── Attaching packages ──────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──✔ ggplot2 3.2.0.9000 ✔ purrr 0.3.2
✔ tibble 2.1.3 ✔ dplyr 0.8.3
✔ tidyr 0.8.99.9000 ✔ stringr 1.4.0
✔ readr 1.3.1 ✔ forcats 0.4.0 ── Conflicts ─────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()library(glue)
Attaching package: 'glue'The following object is masked from 'package:dplyr':
collapsesource("~/Dropbox/Repos/ptb_workflowr/R/config.R")
names_d <- model_df$name
model_terms <- model_df$features
names(model_terms) <- model_df$name
all_feat <- unique(c(unlist(model_terms)))
cc <- drake::drake_cache("/home/nwknoblauch/Dropbox/Repos/ptb_workflowr/cache/rcc4/")
dbdir <-"/home/nwknoblauch/Dropbox/scratch/ptb_scratch/gene_anno/"
drake::loadd(top_gwas_loc,cache=cc)
drake::loadd(top_gwas_reg,cache=cc)
top_regions <- top_gwas_reg$region_id
top_snp <- dplyr::select(top_gwas_loc,min_p=p,region_id=region_id) %>% dplyr::mutate(region_id=as.integer(as.numeric(region_id))) %>% group_by(region_id) %>% summarise(min_p=min(min_p))
fdr_results <- map_df(names_d,function(x){
mutate(drake::readd(glue("fdr_results_.scratch.midway2.nwknoblauch.ptb_scratch.{x}.txt.gz"),character_only = T,cache=cc),model=x)
}) %>% dplyr::select(region_id,fdr,model) %>% inner_join(data_config$data$ld_df) %>% inner_join(top_snp)Joining, by = "region_id"Joining, by = "region_id"spread(fdr_results,key=model,value=fdr) %>% DT::datatable()
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_1.0.0.9000 ldshrink_1.0-1 furrr_0.1.0.9002
[7] future_1.13.0 bigsnpr_0.11.5 bigstatsr_0.9.9
[10] vroom_1.0.2.9000 RSQLite_2.1.1 drake_7.4.0.9000
[13] fs_1.3.1 susieR_0.8.1.0525 here_0.1
[16] dbplyr_1.4.2 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_0.8.99.9000
[25] tibble_2.1.3 ggplot2_3.2.0.9000 tidyverse_1.2.1
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 RcppEigen_0.3.3.5.0 rprojroot_1.3-2
[4] XVector_0.24.0 GenomicRanges_1.36.0 rstudioapi_0.10
[7] listenv_0.7.0 DT_0.7.2 bit64_0.9-7
[10] lubridate_1.7.4 xml2_1.2.2 codetools_0.2-16
[13] knitr_1.23 zeallot_0.1.0 jsonlite_1.6
[16] workflowr_1.4.0 broom_0.5.2 shiny_1.3.2
[19] compiler_3.6.1 httr_1.4.1 backports_1.1.4
[22] assertthat_0.2.1 Matrix_1.2-17 lazyeval_0.2.2
[25] cli_1.1.0 later_0.8.0 htmltools_0.3.6
[28] tools_3.6.1 igraph_1.2.4.1 gtable_0.3.0
[31] GenomeInfoDbData_1.2.1 Rcpp_1.0.2 cellranger_1.1.0
[34] vctrs_0.2.0.9001 nlme_3.1-140 iterators_1.0.10
[37] crosstalk_1.0.0 wavethresh_4.6.8 xfun_0.8
[40] globals_0.12.4 rvest_0.3.4 mime_0.7
[43] lifecycle_0.1.0 zlibbioc_1.30.0 MASS_7.3-51.4
[46] scales_1.0.0 promises_1.0.1 hms_0.5.0
[49] parallel_3.6.1 yaml_2.2.0 memoise_1.1.0
[52] stringi_1.4.3 highr_0.8 S4Vectors_0.22.0
[55] foreach_1.4.4 BiocGenerics_0.30.0 filelock_1.0.2
[58] storr_1.2.2 GenomeInfoDb_1.20.0 rlang_0.4.0.9002
[61] pkgconfig_2.0.2 bitops_1.0-6 evaluate_0.14
[64] lattice_0.20-38 htmlwidgets_1.3 cowplot_1.0.0
[67] bit_1.1-14 magrittr_1.5 R6_2.4.0
[70] IRanges_2.18.1 generics_0.0.2 base64url_1.4
[73] txtq_0.1.3 DBI_1.0.0 pillar_1.4.2
[76] haven_2.1.0 whisker_0.4 withr_2.1.2
[79] RCurl_1.95-4.12 modelr_0.1.4 crayon_1.3.4
[82] rmarkdown_1.13 grid_3.6.1 readxl_1.3.1
[85] data.table_1.12.2 blob_1.1.1 git2r_0.26.1
[88] digest_0.6.20 xtable_1.8-4 httpuv_1.5.1
[91] RcppParallel_4.4.3 stats4_3.6.1 munsell_0.5.0