Implements the method described in "Network-based analysis of omics data: The LEAN method" [Gwinner Boulday (2016) <doi:10.1093/bioinformatics/btw676>] Given a protein interaction network and a list of p-values describing a measure of interest (as e.g. differential gene expression) this method computes an enrichment p-value for the protein neighborhood of each gene and compares it to a background distribution of randomly drawn p-values. The resulting scores are corrected for multiple testing and significant hits are returned in tabular format.
| Version: | 1.4.9 |
| Depends: | R (≥ 2.14), igraph (≥ 0.7.1), foreach (≥ 1.4.2) |
| Suggests: | knitr, doMC, rmarkdown, ROCR, testthat |
| Published: | 2016-11-12 |
| Author: | Frederik Gwinner |
| Maintainer: | Frederik Gwinner <frederik.gwinner at gmail.com> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | LEANR results |
| Reference manual: | LEANR.pdf |
| Vignettes: |
LEAN on CCM data LEAN on simulated subnetworks |
| Package source: | LEANR_1.4.9.tar.gz |
| Windows binaries: | r-devel: LEANR_1.4.9.zip, r-release: LEANR_1.4.9.zip, r-oldrel: LEANR_1.4.9.zip |
| macOS binaries: | r-release (arm64): LEANR_1.4.9.tgz, r-oldrel (arm64): LEANR_1.4.9.tgz, r-release (x86_64): LEANR_1.4.9.tgz, r-oldrel (x86_64): LEANR_1.4.9.tgz |
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