nki-ccb/flexgsea-r

Flexible gene set enrichment analysis

Flexible Gene Set Enrichment Analysis

flexgsea is a R package to do gene set enrichment analysis [1]. Main advantages:

• Allows user defined functions. So you can use you favorite package for differential expression.
• Calculates significance by sample permutation.
• Parallelization using the foreach package.
• Can calculate normalized enrichment scores (NES) and significance based on that.
• Implements the weighted KS-like statistic.

The package is not yet on CRAN. You can install from Github:

# install.packages("devtools")
devtools::install_github("NKI-CCB/flexgsea-r")

Main documentation is on the flexgsea function in the package:

help('flexgsea', 'flexgsea')

This package was called ggsea before.

References

[1] Subramanian, Aravind, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, 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): 15545–50. doi:10.1073/pnas.0506580102.

flexgsea-r's Issues

Error when standard deviation of a gene is 0

Workaround: filter all genes with standard deviation of 0 out before calling ggsea.

Error when running with 0 permutations

Running with 0 permutation can be useful to only compute ES and extra variables for plotting purposes.

Reading of gmt files does do not check input file validity

ggsea_lm should detect cases where the number of samples is larger than the number of variables

The ggsea_lm doesn't work when the number of samples is larger than or equal to the number of variables, it should warn about this.