GSE159526 1.4.0
GSE159526We hope that GSE159526 will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
## Citation info
citation("GSE159526")
#>
#> To cite package 'GSE159526' in publications use:
#>
#> Yuan V, Hui D, Penaherrera M, Beristain A, Robinson W (2021).
#> "Cell-specific characterization of the placental methylome." _BMC
#> Genomics_. doi:10.1186/s12864-020-07186-6
#> <https://doi.org/10.1186/s12864-020-07186-6>,
#> <https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07186-6>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Cell-specific characterization of the placental methylome},
#> author = {Victor Yuan and Desmond Hui and Maria S. Penaherrera and Alexander G. Beristain and Wendy P. Robinson},
#> year = {2021},
#> journal = {BMC Genomics},
#> doi = {10.1186/s12864-020-07186-6},
#> url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07186-6},
#> }GSE159526There are 3 objects associated with GSE159526:
EH6130 - Raw DNA methylation data, .idat files read into r with minfi and
saved as an rgset object.
EH6131 - Processed filtered DNA methylation data. Described in (Yuan, Hui, Penaherrera, Beristain, and Robinson, 2021).
EH6132 - Sample information stored as a tibble/data.frame object.
eh <- ExperimentHub()
query(eh, "GSE159526")
# raw rgset
library(minfi)
GSE159526_rgset <- eh[['EH6130']] # requires minfi
# normalized processed data matrix
GSE159526_data <- eh[['EH6131']]
# sample information
GSE159526_pdat <- eh[['EH6132']]The GSE159526 package (Yuan, Hui, Penaherrera et al., 2021) was made possible thanks to:
This package was developed using biocthis.
Code for creating the vignette:
## Create the vignette
library("rmarkdown")
system.time(render(here::here("vignettes", "GSE159526.Rmd"),
"BiocStyle::html_document"))
## Extract the R code
library("knitr")
knit("GSE159526.Rmd", tangle = TRUE)Date the vignette was generated.
#> [1] "2022-11-03 11:09:12 EDT"Wallclock time spent generating the vignette.
#> Time difference of 0.557 secsR session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23)
#> os Ubuntu 20.04.5 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate C
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2022-11-03
#> pandoc 2.5 @ /usr/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.4.1 2021-12-13 [2] CRAN (R 4.2.1)
#> bibtex 0.5.0 2022-09-25 [2] CRAN (R 4.2.1)
#> BiocManager 1.30.19 2022-10-25 [2] CRAN (R 4.2.1)
#> BiocStyle * 2.26.0 2022-11-02 [2] Bioconductor
#> bookdown 0.29 2022-09-12 [2] CRAN (R 4.2.1)
#> bslib 0.4.0 2022-07-16 [2] CRAN (R 4.2.1)
#> cachem 1.0.6 2021-08-19 [2] CRAN (R 4.2.1)
#> cli 3.4.1 2022-09-23 [2] CRAN (R 4.2.1)
#> digest 0.6.30 2022-10-18 [2] CRAN (R 4.2.1)
#> evaluate 0.17 2022-10-07 [2] CRAN (R 4.2.1)
#> fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.2.1)
#> generics 0.1.3 2022-07-05 [2] CRAN (R 4.2.1)
#> htmltools 0.5.3 2022-07-18 [2] CRAN (R 4.2.1)
#> httr 1.4.4 2022-08-17 [2] CRAN (R 4.2.1)
#> jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.2.1)
#> jsonlite 1.8.3 2022-10-21 [2] CRAN (R 4.2.1)
#> knitr 1.40 2022-08-24 [2] CRAN (R 4.2.1)
#> lubridate 1.8.0 2021-10-07 [2] CRAN (R 4.2.1)
#> magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.2.1)
#> plyr 1.8.7 2022-03-24 [2] CRAN (R 4.2.1)
#> R6 2.5.1 2021-08-19 [2] CRAN (R 4.2.1)
#> Rcpp 1.0.9 2022-07-08 [2] CRAN (R 4.2.1)
#> RefManageR * 1.4.0 2022-09-30 [2] CRAN (R 4.2.1)
#> rlang 1.0.6 2022-09-24 [2] CRAN (R 4.2.1)
#> rmarkdown 2.17 2022-10-07 [2] CRAN (R 4.2.1)
#> sass 0.4.2 2022-07-16 [2] CRAN (R 4.2.1)
#> sessioninfo * 1.2.2 2021-12-06 [2] CRAN (R 4.2.1)
#> stringi 1.7.8 2022-07-11 [2] CRAN (R 4.2.1)
#> stringr 1.4.1 2022-08-20 [2] CRAN (R 4.2.1)
#> xfun 0.34 2022-10-18 [2] CRAN (R 4.2.1)
#> xml2 1.3.3 2021-11-30 [2] CRAN (R 4.2.1)
#> yaml 2.3.6 2022-10-18 [2] CRAN (R 4.2.1)
#>
#> [1] /tmp/RtmpU01XKY/Rinst2e9ff9481ce858
#> [2] /home/biocbuild/bbs-3.16-bioc/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────This vignette was generated using BiocStyle (Oleś, 2022) with knitr (Xie, 2022) and rmarkdown (Allaire, Xie, McPherson et al., 2022) running behind the scenes.
Citations made with RefManageR (McLean, 2017).
[1] J. Allaire, Y. Xie, J. McPherson, et al. rmarkdown: Dynamic Documents for R. R package version 2.17. 2022. URL: https://github.com/rstudio/rmarkdown.
[2] M. W. McLean. “RefManageR: Import and Manage BibTeX and BibLaTeX References in R”. In: The Journal of Open Source Software (2017). DOI: 10.21105/joss.00338.
[3] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.26.0. 2022. URL: https://github.com/Bioconductor/BiocStyle.
[4] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2022. URL: https://www.R-project.org/.
[5] H. Wickham. “testthat: Get Started with Testing”. In: The R Journal 3 (2011), pp. 5–10. URL: https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf.
[6] H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session Information. R package version 1.2.2. 2021. URL: https://CRAN.R-project.org/package=sessioninfo.
[7] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.40. 2022. URL: https://yihui.org/knitr/.
[8] V. Yuan, D. Hui, M. Penaherrera, et al. “Cell-specific characterization of the placental methylome”. In: BMC Genomics (2021). DOI: 10.1186/s12864-020-07186-6. URL: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07186-6.