Last updated: 2024-09-16
Checks: 7 0
Knit directory: rss-gsea/
This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20180626) was run prior to running
the code in the R Markdown file. Setting a seed ensures that any results
that rely on randomness, e.g. subsampling or permutations, are
reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 0d0131b. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish or
wflow_git_commit). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
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 repository in which changes were
made to the R Markdown (analysis/ldl2010_path1698.Rmd) and
HTML (docs/ldl2010_path1698.html) files. If you’ve
configured a remote Git repository (see ?wflow_git_remote),
click on the hyperlinks in the table below to view the files as they
were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | dedfe81 | Xiang Zhu | 2024-09-16 | Build site. |
| html | 7223781 | Xiang Zhu | 2019-02-18 | Build site. |
| html | f5fd9cd | Xiang Zhu | 2018-10-05 | Build site. |
| Rmd | 782d641 | Xiang Zhu | 2018-10-05 | wflow_publish("analysis/ldl2010_path1698.Rmd") |
Prioritization results are summarized by the following table.
P1: posterior probability that at least one SNP within 100 kb of the transcribed region of a given pathway gene (defined by Chr., Start and End columns) has non-zero effect on the trait of interest;
H-distance: the physical distance, in base pair, between a given pathway gene and its nearest GWAS hit;
Nearest hit: the nearest GWAS hit to a given pathway gene, reported in the corresponding GWAS publication.
The “Inf” values in column H-distance indicate that there is no GWAS hit on the same chromosome as the pathway gene.
Differences between Baseline P1 and Enrichment P1 reflect the influence of enrichment on genetic associations, which can help identify putatively trait-associated genes.
| Gene | Chr. | Start | End | Baseline P1 | Enrichment P1 | H-distance | Nearest hit |
|---|---|---|---|---|---|---|---|
| MTTP | 4 | 100485240 | 100545154 | 0.1415537 | 0.9923219 | Inf | none |
| LIPC | 15 | 58724175 | 58861073 | 0.0163921 | 0.9589340 | Inf | none |
| APOA2 | 1 | 161192083 | 161193418 | 0.0033433 | 0.5842822 | 51373777 | rs629301 |
| P4HB | 17 | 79801034 | 79818544 | 0.0000308 | 0.0081494 | 34409230 | rs7225700 |
| SAR1B | 5 | 133936839 | 133968533 | 0.0027561 | 0.4542058 | 22421764 | rs6882076 |
| LPL | 8 | 19796582 | 19824770 | 0.0066880 | 0.7603627 | 10611436 | rs2126259 |
| HSPG2 | 1 | 22148737 | 22263750 | 0.0052681 | 0.6798969 | 3511983 | rs12027135 |
| SDC1 | 2 | 20400558 | 20425194 | 0.0231079 | 0.9153864 | 838706 | rs1367117 |
| LDLRAP1 | 1 | 25870076 | 25895377 | 0.0419188 | 0.8828886 | 94343 | rs12027135 |
| APOA1 | 11 | 116706469 | 116708338 | 0.7034787 | 0.9995003 | 57552 | rs964184 |
| APOC3 | 11 | 116700624 | 116703787 | 0.9998878 | 1.0000000 | 51707 | rs964184 |
| APOA4 | 11 | 116691418 | 116694011 | 0.9998877 | 1.0000000 | 42501 | rs964184 |
| APOC2 | 19 | 45449239 | 45452822 | 1.0000000 | 1.0000000 | 26293 | rs4420638 |
| APOA5 | 11 | 116660086 | 116663136 | 1.0000000 | 1.0000000 | 11169 | rs964184 |
| APOE | 19 | 45409039 | 45412650 | 1.0000000 | 1.0000000 | 10296 | rs4420638 |
| APOB | 2 | 21224301 | 21266945 | 1.0000000 | 1.0000000 | 0 | rs1367117 |
| LDLR | 19 | 11200038 | 11244506 | 1.0000000 | 1.0000000 | 0 | rs6511720 |
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 4.4.1 (2024-06-14)
os macOS Sonoma 14.6.1
system aarch64, darwin20
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Los_Angeles
date 2024-09-16
pandoc 3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
─ Packages ───────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
AnnotationDbi 1.66.0 2024-06-16 [1] Bioconductor 3.19 (R 4.4.0)
Biobase 2.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
BiocFileCache 2.12.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
BiocGenerics 0.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
biomaRt * 2.60.1 2024-06-26 [1] Bioconductor 3.19 (R 4.4.0)
Biostrings 2.72.1 2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
bit 4.0.5 2022-11-15 [1] CRAN (R 4.4.0)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0)
bslib 0.8.0 2024-07-29 [1] CRAN (R 4.4.0)
cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0)
callr 3.7.6 2024-03-25 [1] CRAN (R 4.4.0)
cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.0)
colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.4.0)
crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.0)
curl 5.2.2 2024-08-26 [1] CRAN (R 4.4.1)
DBI 1.2.3 2024-06-02 [1] CRAN (R 4.4.0)
dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.4.0)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.4.0)
digest 0.6.37 2024-08-19 [1] CRAN (R 4.4.1)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.0)
evaluate 0.24.0 2024-06-10 [1] CRAN (R 4.4.0)
fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
filelock 1.0.3 2023-12-11 [1] CRAN (R 4.4.0)
fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0)
GenomeInfoDb 1.40.1 2024-06-16 [1] Bioconductor 3.19 (R 4.4.0)
GenomeInfoDbData 1.2.12 2024-09-16 [1] Bioconductor
getPass 0.2-4 2023-12-10 [1] CRAN (R 4.4.0)
git2r 0.33.0 2023-11-26 [1] CRAN (R 4.4.0)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
highr 0.11 2024-05-26 [1] CRAN (R 4.4.0)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0)
httr2 1.0.4 2024-09-13 [1] CRAN (R 4.4.1)
IRanges 2.38.1 2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.4.0)
jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0)
kableExtra * 1.4.0 2024-01-24 [1] CRAN (R 4.4.0)
KEGGREST 1.44.1 2024-06-19 [1] Bioconductor 3.19 (R 4.4.0)
knitr 1.48 2024-07-07 [1] CRAN (R 4.4.0)
later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.4.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.0)
munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
pkgload 1.4.0 2024-06-28 [1] CRAN (R 4.4.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0)
prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.4.0)
processx 3.8.4 2024-03-16 [1] CRAN (R 4.4.0)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.4.0)
progress 1.2.3 2023-12-06 [1] CRAN (R 4.4.0)
promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.0)
ps 1.8.0 2024-09-12 [1] CRAN (R 4.4.1)
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0)
R.matlab * 3.7.0 2022-08-25 [1] CRAN (R 4.4.0)
R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.4.0)
R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.4.0)
R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.4.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.4.0)
Rcpp 1.0.13 2024-07-17 [1] CRAN (R 4.4.0)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.0)
rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.0)
rmarkdown 2.28 2024-08-17 [1] CRAN (R 4.4.0)
rprojroot 2.0.4 2023-11-05 [1] CRAN (R 4.4.0)
RSQLite 2.3.7 2024-05-27 [1] CRAN (R 4.4.0)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
S4Vectors 0.42.1 2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
sass 0.4.9.9000 2024-07-11 [1] Github (rstudio/sass@9228fcf)
scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
shiny 1.9.1 2024-08-01 [1] CRAN (R 4.4.0)
stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0)
stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
svglite 2.1.3 2023-12-08 [1] CRAN (R 4.4.0)
systemfonts 1.1.0 2024-05-15 [1] CRAN (R 4.4.0)
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
UCSC.utils 1.0.0 2024-05-06 [1] Bioconductor 3.19 (R 4.4.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.0)
usethis 3.0.0 2024-07-29 [1] CRAN (R 4.4.0)
utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.4.0)
whisker 0.4.1 2022-12-05 [1] CRAN (R 4.4.0)
withr 3.0.1 2024-07-31 [1] CRAN (R 4.4.0)
workflowr * 1.7.1 2023-08-23 [1] CRAN (R 4.4.0)
xfun 0.47 2024-08-17 [1] CRAN (R 4.4.0)
xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0)
XVector 0.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
yaml 2.3.10 2024-07-26 [1] CRAN (R 4.4.0)
zlibbioc 1.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
[1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
──────────────────────────────────────────────────────────────────────────────