parseGmt: Venn Euler Diagramm

In GiANT: Gene Set Uncertainty in Enrichment Analysis

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

GiANT documentation built on Oct. 23, 2020, 7:56 p.m.