LEANR-package:
Finds "local subnetworks" within an interaction network which show enrichment for differentially expressed genes
Description
Implements the method described in "Network-based analysis of omics data: The LEAN method".
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.
Details
|
Package: |
| LEANR |
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Type: |
| Package |
|
Version: |
| 1.4.8 |
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Date: |
| 2016-11-11 |
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License: |
| GPL-3 |
See help page of run.lean for a more detailed description of how to use this package.
Type vignette("CCM-data") for an example showing the application of LEAN to the CCM knockout data set discussed in the paper.
Type vignette("subnet-sim") for an example showing the application of LEAN to simulated subnetwork data discussed in the paper.
References
Gwinner et al., Network-based analysis of omics data: The LEAN method, Bioinformatics 2016
See Also
run.lean
vignette("CCM-data")
vignette("subnet-sim")