Single-sample GSEA 2.0

The R-scripts ssgsea-gui.R and ssgsea-cli.R provide wrapper to the ssGSEA R-program which performs the actual single sample Gene Set Enrichment analysis (ssGSEA). ssgsea-cli.R can be executed from the command line, please see ssgsea-cli.R --help for instructions.

Instructions to run ssgsea-gui.R

Windows OS

To run the script source it into a running R-session.

• RStudio: open the file and press 'Source' in the upper right part of the editor window
• R-GUI: drag and drop this file into an R-GUI window

Input files and databases can be specified via Windows file dialogs that will be automatically invoked. The first dialog lets you choose a folder containing input files in GCT v1.2 or GCT v1.3 format. The script loops over all GCT files in this directory and runs ssGSEA on each file separately. The second dialog window lets the user choose one or multiple gene set databases in GMT format such as MSigDB. A current version of MSigDB databases can be found in the db subfolder.

iOS/MAC

In order to invoke file dialogs as decribed above, the XQuartz X Window System is required. Once installed ssgsea-gui.R can be sourced into an R session.

ssGSEA parameters

Other paramaters for ssGSEA can be altered inside the parameters section in ssgsea-gui.R. The default parameters have been choosen carefully and should provide reliable results for most use-case scenerios.

Gene Set Enrichment Analysis (GSEA)

For information about the method please visit http://software.broadinstitute.org/gsea/.

Changes to the original ssGSEA implementation

Original code written by Pablo Tamayo. Adapted with additional modifications by D. R. Mani and Karsten Krug. Adaptions include:

• support of multiple CPU cores (doParallel R-package)
• support of GCT v1.3 format using functions from cmapR
• improved handling of missing values
• scoring of directional gene sets
• basic error handling
• general performance improvements
• additional output files like rank plots and parameter files

References

1. Abazeed, M. E., Adams, D. J., Hurov, K. E., Tamayo, P., Creighton, C. J., Sonkin, D., et al. (2013). Integrative Radiogenomic Profiling of Squamous Cell Lung Cancer. Cancer Research, 73(20), 6289-6298. http://doi.org/10.1158/0008-5472.CAN-13-1616

2. Barbie, D. A., Tamayo, P., Boehm, J. S., Kim, S. Y., Susan, E., Dunn, I. F., . Hahn, W. C. (2010). Systematic RNA interference reveals that oncogenic KRAS- driven cancers require TBK1, 462(7269), 108-112. https://doi.org/10.1038/nature08460

3. Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., et al. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America, 102(43), 15545-15550. http://doi.org/10.1073/pnas.0506580102

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