GSE159526 1.0.0
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")
#>
#> 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 (URL:
#> https://doi.org/10.1186/s12864-020-07186-6), <URL:
#> 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] "2021-10-30 11:22:22 EDT"Wallclock time spent generating the vignette.
#> Time difference of 0.678 secsR session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.1.1 (2021-08-10)
#> os Ubuntu 20.04.3 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate C
#> ctype en_US.UTF-8
#> tz America/New_York
#> date 2021-10-30
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> package * version date lib source
#> BiocManager 1.30.16 2021-06-15 [2] CRAN (R 4.1.1)
#> BiocStyle * 2.22.0 2021-10-29 [2] Bioconductor
#> bookdown 0.24 2021-09-02 [2] CRAN (R 4.1.1)
#> bslib 0.3.1 2021-10-06 [2] CRAN (R 4.1.1)
#> cli 3.1.0 2021-10-27 [2] CRAN (R 4.1.1)
#> digest 0.6.28 2021-09-23 [2] CRAN (R 4.1.1)
#> evaluate 0.14 2019-05-28 [2] CRAN (R 4.1.1)
#> fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.1.1)
#> generics 0.1.1 2021-10-25 [2] CRAN (R 4.1.1)
#> htmltools 0.5.2 2021-08-25 [2] CRAN (R 4.1.1)
#> httr 1.4.2 2020-07-20 [2] CRAN (R 4.1.1)
#> jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.1.1)
#> jsonlite 1.7.2 2020-12-09 [2] CRAN (R 4.1.1)
#> knitr 1.36 2021-09-29 [2] CRAN (R 4.1.1)
#> lubridate 1.8.0 2021-10-07 [2] CRAN (R 4.1.1)
#> magrittr 2.0.1 2020-11-17 [2] CRAN (R 4.1.1)
#> plyr 1.8.6 2020-03-03 [2] CRAN (R 4.1.1)
#> R6 2.5.1 2021-08-19 [2] CRAN (R 4.1.1)
#> Rcpp 1.0.7 2021-07-07 [2] CRAN (R 4.1.1)
#> RefManageR * 1.3.0 2020-11-13 [2] CRAN (R 4.1.1)
#> rlang 0.4.12 2021-10-18 [2] CRAN (R 4.1.1)
#> rmarkdown 2.11 2021-09-14 [2] CRAN (R 4.1.1)
#> sass 0.4.0 2021-05-12 [2] CRAN (R 4.1.1)
#> sessioninfo * 1.1.1 2018-11-05 [2] CRAN (R 4.1.1)
#> stringi 1.7.5 2021-10-04 [2] CRAN (R 4.1.1)
#> stringr 1.4.0 2019-02-10 [2] CRAN (R 4.1.1)
#> withr 2.4.2 2021-04-18 [2] CRAN (R 4.1.1)
#> xfun 0.27 2021-10-18 [2] CRAN (R 4.1.1)
#> xml2 1.3.2 2020-04-23 [2] CRAN (R 4.1.1)
#> yaml 2.2.1 2020-02-01 [2] CRAN (R 4.1.1)
#>
#> [1] /tmp/RtmpgobCW3/Rinst222750aacb0b2
#> [2] /home/biocbuild/bbs-3.14-bioc/R/libraryThis vignette was generated using BiocStyle (Oleś, 2021) with knitr (Xie, 2021) and rmarkdown (Allaire, Xie, McPherson, et al., 2021) 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 2.11. 2021. URL: https://github.com/rstudio/rmarkdown.
[2] G. Csárdi, R. core, H. Wickham, et al. sessioninfo: R Session Information. R package version 1.1.1. 2018. URL: https://CRAN.R-project.org/package=sessioninfo.
[3] 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.
[4] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.22.0. 2021. URL: https://github.com/Bioconductor/BiocStyle.
[5] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2021. URL: https://www.R-project.org/.
[6] 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.
[7] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.36. 2021. 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.