parse GMT files {GiANT} | R Documentation |
Parses a GMT file as downloadable from MSigDB (presented in Subramanian et al.) and returns a list of gene sets.
parseGmt(file)
file |
A file name. |
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.
A named list
of gene sets.
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.
geneSetAnalysis
, predefinedAnalyses
, gsAnalysis