write.ls.to.sif

local.subnetwork.export


    protein id compatible with node names used in graph <code>g</code>


prot_id


    LEAN result object (list) returned by <run.lean> or <run.lean.fromdata>
</run.lean.fromdata></run.lean>

LEANres


  character string describing the location of an output file. Should end in .sif to be able to load it in Cytoscape.


outfile


 Extract the "local subnetwork" around a given protein and write it to a Cytoscape-readable .sif file


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.

Frederik Gwinner

LEANR

Finds "Local Subnetworks" Within an Interaction Network which
Show Enrichment for Differentially Expressed Genes

write.ls.to.sif function


    LEAN result object (list) returned by <run.lean> or <run.lean.fromdata>


write.ls.to.sif: Extract the "local subnetwork" around a given protein

Description

Usage

Arguments

See Also