parse GMT files {GiANT} | R Documentation |
Venn Euler Diagramm
Description
Parses a GMT file as downloadable from MSigDB (presented in Subramanian et al.) and returns a list of gene sets.
Usage
parseGmt(file)
Arguments
file |
A file name. |
Details
Parses a GMT file and returns a list of gene sets. Each list element named according to the included gene set. The gene set files can be downloaded from http://www.broadinstitute.org/gsea/msigdb.
Value
A named list
of gene sets.
References
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., Mesirov, J. P. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Science of the United States of America, 102, 15545–15550.
See Also
geneSetAnalysis
, predefinedAnalyses
, gsAnalysis