1 / 16

Using R for Data Analysis

Using R for Data Analysis. Course December 2010 Jelle Goeman Ren é e de Menezes. Packages. Packages: community created functions. Finding packages:. CRAN: Comprehensive R archive network http://cran.r-project.org/web/packages/ General repository for R packages 2390 packages available

chill
Download Presentation

Using R for Data Analysis

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Using R for Data Analysis Course December 2010 Jelle Goeman Renée de Menezes

  2. Packages R Course

  3. Packages: community created functions R Course

  4. Finding packages: • CRAN: Comprehensive R archive network • http://cran.r-project.org/web/packages/ • General repository for R packages • 2390 packages available • Bioconductor • www.bioconductor.org • R Packages related to genomics • 389 packages available R Course

  5. Package website: CRAN R Course

  6. Package website: bioconductor R Course

  7. Acquiring a package • Acquiring a package requires two steps: • Install: • Makes the package available on your PC • Do once (repeat if you have a new R version) • Load: • Makes the package available in your current R session • Do every time you use a package R Course

  8. Install: by menu • Download zip file for your operating system • Install using menu • Packages… Install package from local zip file R Course

  9. Install from prompt • Traditional way: > install.packages("penalized") • Recommended: use biocLite script > source("http://bioconductor.org/biocLite.R") > biocLite("globaltest") • Advantages of biocLite: • Automatically installs dependencies • Installs proper package version for your R version • Works for both CRAN and Bioconductor R Course

  10. What does a package do? Vignettes • Many packages have a “Vignette” = manual • Obtain via package site • Or use the vignette command # list of all vignettes > vignette() # list of vignettes for a specific package > vignette(package="globaltest") # open a specific vignette > vignette("GlobalTest") R Course

  11. Vignette and Reference manual R Course

  12. What does a package do? Help files • Overview of a package’s help files • Go to menu…help…html help…packages • Obtain list of packages. Below: list of help files in the package R Course

  13. Example: lumi probe annotation package R Course

  14. Loading a package • Make the package’s functions available in the current R session > library(globaltest) > require(globaltest) R Course

  15. Finding a package: CRAN task views R Course

  16. Finding a package: Bioconductor task views R Course

More Related