LEANR-package: Finds "local subnetworks" within an interaction network which...

In LEANR: 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
Type:	Package
Version:	1.4.8
Date:	2016-11-11
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.

Author(s)

Frederik Gwinner

Maintainer: Frederik Gwinner <[e-mail]>

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")

LEANR documentation built on May 2, 2019, 3:46 p.m.