Reproducible Research resources for NBIS LT project j_lehtio_1411
This is a collaborative project between the Janne Lehtiö group, Department of Oncology-Pathology, Karolinska Institutet and the NBIS long-term support (a.k.a. WABI), performed during 2015-2018 (NBIS LT project name: J_Lehtio_1411).
As a part of the NBIS reproducible research policy, this repository provides the data-files and R-scripts necessary to perform the underlying analyses and create tables and plots ued in Johansson et al. Breast cancer quantitative proteome and proteogenomic landscape (manuscript in prep; link not yet available)
More specifically, the script FinalFigures.Rmd reproduces parts of Main text figure 5, and Supplementary figure S5 and Suppementary Table S3 (as well as some additional figures not used in the manuscript).
Note! The repository is provided for reproducibility reasons, only; no further development will be made.
The content of this repository can be obtained in two ways:
Download the current release as a zip- or tar-archive (e.g., by
clicking Download Zip File or Download TAR Ball on the
github.io page)
Clone the repository from the github page (reached from the
github.io page by clicking View on GitHub)
The easiest way of running the script is to open FinalFigures.Rmd
in Rstudio, set the working directory (menu ‘Session | Set Working
Directory’ for MacOSX or ‘Tools|Change Working Dir…’ else) to ‘To
Source File Location’, and then press the knit button.
Alternatively, the following commands can be issued inside a R-environment (command-line or script) in the downloaded directory:
require(rmarkdown)
render('FinalFigures.Rmd')
Note: it seems like this alternative requires (at least) pandoc to be installed (e.g., using macports).
The script are designed to install required R-packages as needed; however, this feature has not been tested extensively on different operative systems (scripts were developed on MacOSX).
The two .RMD documents perform the main analyses in this repository. They double as the main documentation tool:
These are called by the main R-file
formatData.R R-script that reads the data files obtained from Henrik Johansson, Lehtio’s group (usually in Excel format), reformat data to format useful in the present analyses, and save them as a R-object, for later use in .Rmd-files.