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.
|Date of publication||2016-11-12 15:47:01|
|Maintainer||Frederik Gwinner <firstname.lastname@example.org>|
CCM.pvals: Gene p-value list derived from knock-out experiments of the...
g2: igraph graph object used in examples for function...
gene.annots: Annotation for STRING protein Ids
gene.list.scores: Gene p-value list used in examples for function...
get.ls.info: Extract the genes of a "local subnetwork"" around a given...
g_red: igraph graph object used in unit tests
LEANR-package: Finds "local subnetworks" within an interaction network which...
pvals_red: Gene p-value list used in unit tests
run.lean: Run the LEAN approach
subnet.simulation: Simulate subnetworks
write.ls.to.sif: Extract the "local subnetwork" around a given protein